NAD-binding domains of dehydrogenases

Arthur M Lesk

U n i v e r s i t y of C a m b r i d g e Clinical School, C a m b r i d g e , U K

The nicotinamide adenine dinucleotide (NAD)-binding domains of dehydro-

genases, containing a conserved double ~-et-[~-a-~ motif, are a common
structural feature of many enzymes that bind NAD, nicotinamide adenine
dinucleotide phosphate (NADP) and related cofactors. Features of this folding
pattern that create a natural binding site for such molecules have been
described. The domain continues to appear in many structures, in the
form of a common core with different peripheral additions or variations.
Other structures that bind NAD and related molecules use entirely different
topologies, although, in many, a phosphate group appears at the N terminus
of an a helix. Ferredoxin reductase seems to show convergent evolution,
containing a single [3-a-[3 motif that is similar both in its structure and in its
interactions with the ligand to a region in dehydrogenases.

Current Opinion in Structural Biology 1995, 5:775-783

Introduction known: lactate, malate, alcohol and glyceraldehyde-3-

Twenty years ago, the principle had already been
recognized that protein structures could show topo-
logical similarity in general but divergence in struc-
tural details. Early examples included globins (myo-
globin, haemoglobin and Chironomus erythrocruorin),
chymotrypsin-like serine proteases, and NAD-binding
domains.
In 1970, Adams et al. [1] published the first description
of a dehydrogenase structure, that of lactate dehydroge-
nase from dogfish (Sclualus acanthus). Bdind~n and P,.oss-
mann [2] then compared the dogfish lactate dehydroge-
nase structure with a prehminary low-resolution struc-
ture of horse liver alcohol dehydrogenase, and observed
a basic resemblance between the NAD-binding domains
(for early history, see [3]). Subsequently, Rao and P,.oss-
mann [4] developed systematic methods for comparison
ofsupersecondary structures and applied them to the de-
hydrogenases and flavodoxin.
In 1973, knowing the structures of the lactate, malate
and alcohol dehydrogenases, Bfiind~n et al. [5] wrote
"The coenzyme binding region [of horse liver alco-
hol dehydrogenase] has a main-chain conformation very
similar to a corresponding region in lactate and malate
dehydrogenase. It is suggested that this substructure is a
general one for binding of nucleotides and, in partic-
ular, the coenzyme NAD +''. By the end of 1973, the
structures of four NAD-binding dehydrogenases were
phosphate dehydrogenases. In 1974, lq.ossmann, Moras
and Olsen [6] showed that: "Three-dimensional struc-
tural alignment of the common nucleotide binding
structure in dehydrogenases, kinases and flavodoxins per-
mits the recognition of homologous amino acids when
sequence comparisons alone would fail".
Since then, many additional crystal structures have con-
firmed and extended these principles. Table 1 lists the
NAD-binding domains of dehydrogenases distributed in
the Protein Data Bank (PDB) [7] as classified in the
structural classification of proteins (SCOP) [8"]. There
are now a total of eleven different enzymes in the PDB,
and crystal structures exist from more than one species
for five of them. For several of the enzymes, structures
have been determined in different states ofligation. Dur-
ing the past two years, there were fourteen new PDB en-
tries. In four of these cases (for 30c,20[~-hydroxysteroid
dehydrogenase, formate dehydrogenase, 6-phosphoglu-
conate dehydrogenase and quinone oxidoreductase) no
crystal structure had previously been deposited.
Other proteins bind nucleotide-containing cofactors in
a manner similar to that observed for the binding of
dehydrogenases to NAD, and they create the binding
site from domains with generally similar secondary and
tertiary structure. Examples include the binding offlavo-
doxin to FMN and the binding of pyruvate oxidase to
FAD. Br~ind~n [9] described how the folding pattern of
NAD-binding domains and related structures creates a

Abbreviations
ADH--alcohol dehydrogenase; FAD--flavin adenine dinucleotide; FMN--flavin mononucleotide;
NAD--nicotinamide adenine dinucleotide; NADP--nicotinamide adenine dinucleotide phosphate;
PDB--Protein Data Bank; SCOP--structural classification of proteins.

© Current Biology Ltd ISSN 0959-440X 775

776 Proteins

Table 1. List of crystal structures of enzymes containing NAD-binding domains.

Enzyme PDB code Source Resolution (,g,) R-factor Year
Alcohol dehydrogenase 5adh Horse liver 2.9 1984
6adh Horse liver 2.9 1984
7adh Horse liver 3.2 0.290 1984
8adh Horse liver 2.4 0.190 1989
2ohx Horse liver 1.8 0.173 1993
1hid Horse liver 2.1 0.183 1993
2oxi Horse liver 2.1 0.160 1993
ladg Horse liver 2.7 0.160 1993
1adf Horse liver 2.9 0.150 1993
1hdx Human 2.5 0.179 1993
1hdy Human 2.5 0.185 1992,
3hud Human 3.2 0.179 1993
1hdz Human 2.45 0.194 1993

3c~,2013-hydroxysteroid dehydrogenase 1hdc Streptomyces hydrogenans 2.2 0.194 1994

2hsd Streptomyces hydrogenans 2.64 0.188 1994

Dihydropterin reductase 1dhr Rat liver 2.3 1992

ldir Rat liver 2.6 1994
lhdr Human 2.5 0.169 1993

Uridine diphosphogalactose-4- 1udp Escherichia coli 2.5 0.184 1992

epimerase

Glyceraldehyde-3-phosphate 1gpd Lobster 2.9 1975

dehydrogenase 3gpd Human 3.5 0.330 1983
4gpd Lobster 2.8 0.218 1988
1gd 1 Bacillus stearothermophilus 1.8 0.177 1987
2gdl Bacillus stearothermophilus 2.5 0.177 1989
1gga Trypanosoma brucei brucei, glycosome 3.2 0.176 1991
1hdg Thermotoga maritima 2.5 0.166 1995

Formate dehydrogenase 2nac Pseudomonas sp. 101 1.8 0.146 1994

formate dehydrogenase Pseudomonas sp. 101 2.0 0.114 1994

D-glycerate dehydrogenase 1gdh Hyphomicrobium methylovorum 2.4 0.189 1993

Malate dehydrogenase 4mdh Pig heart 2.5 0.167 1989

2cmd Escherichia coil 1.87 0.188 1992
1emd Escherichia coli 1.9 0.195 1993
1bmd Thermus flavus, strain at-62 1.9 0.154 1992
1bdm Thermus flavus, strain f428 1.8 0.169 1993
1hip Haloarcula marismortui 3.2 0.182 1994
1mid Pig mitochondria 1.9 0.211 1994

Lactate dehydrogenase 31dh Dogfish muscle 3.0 1974

51dh Pig heart 2.7 0.196 1980
21dx Mouse testicles 2.96 0.256 1987
11dm Dogfish muscle 2.1 0.173 1987
61dh Dogfish muscle 2.0 0.202 1987
81dh Dogfish muscle 2.8 0.191 1988
91dt Porcine muscle 2.0 0.233 1991
91db Porcine muscle 2.2 0.220 1991
1Idn Bacillus stearothermophilus 2.5 0.157 1991
1[db Bacillus stearothermophilus 2.8 0.286 1989
21db Bacillus stearothermophilus 3.0 0.260 1989
1IIc Lactobacillus casei 3.0 0.374 1989
1lid Bifidobacterium Iongum, strain am101-2 2.0 0.179 1992
1Ith Bifidobacterium Iongum 2.5 0.188 1995

6-phosphogluconate dehydrogenase 2pgd Sheep 2.0 0.198 1994

1pgn Sheep 2.3 0.204 1994
1pgo Sheep 2.5 0.170 1994
1pgp Sheep 2.5 0.170 1994
1pgq Sheep 3.17 0.169 1994

Quinone oxidoreductase 1qor2 Escherichia coli 2.2 0.140 1995

binding site. Wierenga, Hol and colleagues ([10,11];
see also [12]) examined protein-dinucleotide interac-
tions and described common patterns in the structures
and the sequences.
Newly elucidated structures have greatly extended our
knowledge of modes of binding of N A D and related
ligands, and have been classified by Brenner et al, [13°].
Some of these structures have very different folding
patterns from those of the NAD-binding domains in
dehydrogenases. They include proteins from other gen-
eral topological classes: all-[~ and 0t+~ proteins, as well as
proteins in the ot/[~ class unrelated to those with the de-
hydrogenase NAD-binding fold. In ferredoxin reductase,
 NAD-bindingdomainsof dehydrogenasesLesk 777

(a)

(b)

Fig. 1. Horse liver alcohol dehydro-

genase. (a) NAD-binding domain. (b)
6 5 4 1 2 3 Hydrogen-bonding pattern of the single,
parallel [3 sheet.

.. 271 Are

224 lie 294 Val 224 lie 294 Val

"" ... ..'" 317 Ala

Fig. 2. Interaction between cofactor (rep-

202 Gly
however, a part of the binding site that is quite similar in
structure to a region o f the dehydrogenases is achieved
in the context of a different folding pattern. This is a
presumptive case of convergent evolution.
Basic structural features of NAD-binding
domains of dehydrogenases
The paradigm nucleotide-binding domain can be illus-
trated by horse liver alcohol dehydrogenase (Fig. 1) [14].
resented as ball-and-stick diagram) and
202 Gly NAD-binding domain in horse liver alco-
hol dehydrogenase.
It is well known that the domain contains two sets
o f ~-0~-~-~-~ units, together forming a single parallel
sheet flanked by 0~ helices. In Figure 1, the strands
appearing from left to right are in the order 6-5-4-1-2-3.
There is a long loop, or cross-over, between strands
3 and 4. This creates a natural cavity that participates
in the binding of the adenine ring of the NAD and, in
other molecules with similar supersecondary structures,
of other nucleotide-containing fragments [9].
The binding of the NAD involves numerous hydrogen
bonds and van der Waals contacts between the cofactor
and the enzyme. Figure 2 shows the interactions of the
778 Proteins

(a)

(b) .7...(
)
.-.---.>-~
-.-.---~ ~*. % % %

{
....

(
( Fig. 3. 6-phosphogluconate dehydroge-
nase (lpgo). (a) NAD-binding domain.
6 5 4 1 2 3 (b) Hydrogen-bonding pattern of the sin-
gle, parallel [3 sheet.

NAD and the domain of alcohol dehydrogenase (ADH)
in more detail. In particular, there are usually hydrogen
bonds, from the residues in the turn between the first
strand and the helix that follows it, to one of the
phosphate groups of the cofactor. These interactions give
rise to a consensus sequence in this region containing
the three-glycine pattern GXGXXG, where X is any
other anfino acid [9-12]. The first two glycines are
involved in nucleotide binding and the third, which
is in the helix following the first strand, is involved
in the packing of the helix against the [3 sheet [9,10].
In most dehydrogenases there is a highly (but not
absolutely) conserved aspartate approximately 20 residues
C-terminal to the G X G X X G motif. This aspartate
appears near the C terminus of the second [3 strand,
and forms hydrogen bonds to the ribose of the adenosine
moiety of the NAD. Residues from the C terminus of
the fifth strand (second from the left in Fig. 1) interact
with the nicotinamide ring and usually form hydrogen
bonds to the amide group.
All the dehydrogenase structures now known contain
a core of similar topology, but show variations on the
common structural theme. I examined these similarities
and differences in eight structures, each containing
NAD or NADE These comprised the four 'classical'
examples (although the coordinate sets chosen are
recently determined ones) lactate dehydrogenase (pig;
PDB code 91dt) [15], malate dehydrogenase (Escherichia
coil PDB code lemd) [16], alcohol dehydrogenase
(horse liver; PDB code 2ohx) [14], and glyceraldehyde-
3-phosphate dehydrogenase (Bacillus stearothermophilus;
PDB code lgdl) [17] and four examples from 'the
next generation': 6-phosphogluconate dehydrogenase
(sheep; PDB code lpgo) [18"], 30t,20[~-hydroxysteroid
dehydrogenase (Streptomyces hydrogenans; PDB code 2hsd)
[19], dihydropteridin reductase (rat liver; PDB code
ldhr) [20], and formate dehydrogenase (Pseudomonas sp.
101; PDB code 2nad) [21].
Comparison of selected dehydrogenase
structures
Figures 1-4 illustrate four of the selected molecules,
showing the folding of the chain and the hydrogen-
bonding net of the sheet. In each picture the chain
can be visually traced and compared with the others (the
direction of the herringbone pattern gives the direction
of the strand).
In all these domains, the sheets contain the canon-
ical six strands, but in dihydropteridme reductase,
glycerddehyde-3-phosphate dehydrogenase, 30~,20~-hy-

(a)
(b)
6 5 4 1 2 3
droxysteroid dehydrogenase, formate dehydrogenase and
6-phosphogluconate dehydrogenase they are extended
by additional strands. Dihydropteridine reductase has
a seventh strand adjacent and parallel to the sixth
strand and an eighth strand forming a hairpin with
the seventh. Formate dehydrogenase and 6-phospho-
gluconate dehydrogenase each have a seventh strand
adjacent and parallel to the sixth, but no eighth strand.
Glyceraldehyde-3-phosphate dehydrogenase has a short
stretch ofantiparallel sheet between the third and fourth
strand, before the cross-over. Finally, 30t,2013-hydroxys-
teroid dehydrogenase has a seventh strand adjacent and
parallel to the sixth, the significance o f which has not
yet been determined.
NAD-binding domainsof dehydrogenasesLesk 779
Fig. 4. Dihydropteridine reductase (ldhr).
(a) NAD-binding domain. (b) Hydrogen-
bonding pattern of single, parallel I~
sheet.
The helices also differ considerably in length, and can
shift relative to the sheet. In 3ct,20[~-hydroxysteroid
dehydrogenase and dihydropteridine reductase the two
helices in the C-terminal portion of the domain
(between strands 4 and 5 and between strands 5 and 6)
are very elongated. There is also a helix in the cross-over
region (the loop between strands 3 and 4) which
is often observed. The cross-over region is especially
variable in structure among the different enzymes.
Dihydropteridine reductase has lost the helix between
strands 2 and 3.
As an example of the conservation of the core
of the structure, Figure 5 shows the superposition
780 Proteins

(a) .".......

Z'

,, ",,,

(b) ~'- ,....... : ;"--. """; "

Fig. 5. Superposition of NAD-binding do-

mains. (a) Lactate dehydrogenase (91dr;
solid lines) and malate dehydrogenase
(lemd; broken lines). The sequence of
residues in these regions have 23% iden-
tity upon optimal alignment. Although
these molecules have developed differ-
ent functions, they are still fairly closely
related. (b) Horse liver alcohol dehydro-
genase (solid lines) and dihydropteri-
dine reductase (1 dhr; broken lines). These
. ..'-k .... " molecules have diverged more radically.
.,. . . . . . . . ',. . . . . . . .
These residues have only 14% identity
upon optimal alignment.

of NAD-binding domains of a closely related pair
(lactate and malate dehydrogenases) and a more distantly
related pair (alcohol dehydrogenase and dihydropteridine
reductase) of enzynles.
The conformation and interactions of the cofactor
differ among the structures. Most, but not all, show
common interactions in the form of hydrogen bonds
between the pyrophosphate of the cofactor and the
region of conserved sequence between the frst strand
and helix (compare Fig. 2) In 6-phosphogluconate
dehydrogenase, however, these hydrogen bonds are
absent. Nevertheless, the structure and sequence pattern
are largely conserved. In addition, the aspartate that
forms hydrogen bonds to the ribose is replaced by
asparagine in 6-phosphogluconate dehydrogenase. This
is significant for the mechanism of discrimination
between NAD and NADP binding sites.

Fig. 6. A comparison of the structures

alcohol dehydrogenase
quinone oxidoreductase
comnlon
TCAVFGL-GGVGLSVIMGCKAAGAARI IGVDINK DKFAKAKEVGA
QFLFHAAAGGVGLIACQWAKALGA-KLIGTV GTAQKAQSALKAGA
of E. coli quinone oxidoreductase with
GGVGL KA GA IG K A GA horse liver alcohol dehydrogenase, show-
ing the residues they have in con~mon.

Fig. 7. Superposition of regions interact-

ing with adenosine unit of NAD in horse
liver alcohol dehydrogenase (2ohx; solid
line), and the adenosine unit of NADP
in quinone oxidoreductase (1 qor; broken
line).

. . . < ~ 6PGDH
(b)
~:'... ..
-"-..." ",:,-
,.., ,'.<.. I ~
.::"
.." :, ,/
............... ! ....................i
The s e q u e n c e m o t i f G X G X X G
The sequence GXGXXG is characteristic of'the first [3-
ct-[3 unit in the dehydrogenase domain [9,10]. The first
glycine is in a ++quadrant of the P, amachandran plot
integral to the structure of the turn. A [~-carbon (C[~) at
the position of the second glycine would collide with the
cofactor. The third glycine is in the helix following the
first strand, and allows for packing of the helix against
the sheet. In horse liver alcohol dehydrogenase, a C[~ in
the residue at the position of the third glycine would
clash with the carbonyl group of the first glycine.
Four of the structures considered contain the GXGXXG:
lactate dehydrogenase, glyceraldehyde-3-phosphate de-
hydrogenase, alcohol dehydrogenase, and dihydropteridin
reductase. Two other structures contain an alanine
instead of the first glycine: malate and fornmte dehydro-
genases. In forlnate dehydrogenase (2had), the alanine
is in a ++ conformation. In malate dehydrogenase
NAD-binding domains of dehydrogenases Lesk 781
6PGDH
Fig. 8. Superposition of regions inter-
acting with adenosine unit of NAD in
horse liver alcohol dehydrogenase (2ohx;
solid line), and the adenosine unit of
NADP in 6-phosphogluconate dehydro-
genase (1 pgo; broken line).
:~.... ...
--a---,, " - .: -.-,-
i i ~ ] "
" ~: ]
Fig. 9. Ferredoxin reductase (lfnd). (a)
General structure of the NADP-binding
domain, showing a different folding pat-
tern from dehydrogenase domains. (b)
Superposition of ~-ct-~ units from lac-
tate dehydrogenase (91dt; solid line) and
ferredoxin reductase (lfnd; broken line),
.,
:" showing cofactor NAD (solid line) for
lactate dehydrogenase and inhibitor 2'-
phospho-AMP (broken line) for ferre-
doxin reductase.
(lemd) the alanine is preceded by a glycme in a ++
conformation, and a structural superposition shows that
the alanine is an insertion into the loop and causes only
local defbrmation of the chain. An alanine is at the
position of the second glycine in 6-phosphogluconate
dehydrogenase. In this structure, which binds NADR
the usual interaction between the first [~-0t-[~ unit
and the pyrophosphate is absent (see below). In
3c<20[~-hydrox2csteroid dehydrogenase (2hsd), there is
also an insertion in the loop; a structural superposition
of this structure onto alcohol dehydrogenase gives the
alignment:
alcohol dehydrogenase TCAVFGL-GGVGL
3¢z,20[~-hydroxvsteroiddehydrogenase TVIITGGARGLGA
This sequence pattern is characteristic of the short-chain
dehydrogenase family [19,22].
782 Proteins
Binding of NAD and NADP
Several structures are now known that contain most
elements o f the standard NAD binding site, but bind
NADP instead. In dehydrogenase domains that bind
NAD, the space that would be taken up by the extra
phosphate of NADP is occupied by the conserved
hydrogen bond between the aspartate in the binding
site (Asp223 in horse liver alcohol dehydrogenase) and
the adenosine ribose of the NAD.
A comparison of the structures of IF,. colt quinone
oxidoreductase (cofactor NADP) [23"] and horse liver
alcohol dehydrogenase (cofactor NAD) shows an ad-
justment in this region (Fig. 6; the asterisk marks the
position of the conserved aspartate in NAD-binding
enzymes). The structures of the first [~-ot-~-ot unit are
quite similar (Fig. 7).
Figure 7 shows that there has been a conformational
change in the loop that connects the second strand
and the second helix. In place of the Asp223-ribose
hydrogen bond in alcohol dehydrogenase, there is a
hydrogen bond between the nitrogen of Gly173 and
a phosphate oxygen. Note that the phosphate oxygen
occupies the same region as the aspartate does in the
NAD-binding enzyme; this can be considered to be an
example o f a 'complementary mutation', as is sometimes,
albeit rarely, observed in protein evolution.
An alternative way of accommodating NADP is seen
in the structure o f 6-phosphogluconate dehydrogenase
(Fig. 8). An asparagine appears at the position occupied
by the conserved aspartate in NAD-binding dehydro-
genases, and forms hydrogen bonds to the phosphate as
well as to the sugar of the NADR As a result the cofactor
moves away from the domain, breaking the interaction
between the pyrophosphate and the loop at the end of
the first [3 strand.
Ferredoxin reductase: a case of partial
convergence
The relationship between the NADP-binding site of
ferredoxin reductase and the dehydrogenases is illustrated
in Figure 9. Ferredoxin reductase was crystallized with
a competitive inhibitor (2'-phospho-AMP) that defines
the NADP+-binding site [24]. The structure has two
domains; one binds FAD in a [~ sheet structure, and the
other binds NADE Figure 9a shows the general structure
of the NADP-binding domain and the placement of
the inhibitor. Although the domain differs in its overall
fold from the NAD-binding domains of dehydrogenases,
there is a single I~-ct-~ unit that is likely to interact
with the pyrophosphate of the NADP. Figure 9b
shows a superposition of the analogous units from
lactate dehydrogenase (91dt; solid lines) and ferredoxin
reductase (lfnd; broken lines), and their ligands (NAD
and 2'-phospho-AMP respectively; compare with Fig. 5
of [241).
Conclusions
The repertoire of structures that bind NAD and related
cofactors has been increasing in number and scope (see
Table 1). Many enzymes have been observed to contain
the classical NAD-binding domain of dehydrogenases,
although other modes o f NAD and NADP binding
have also appeared. The structures confirm the basic
ideas about how the widely conserved IB-0~-13-~-I~ fold
achieves its function as described by Br~nd6n ill 1980
[9], and enable us to analyze the detailed nlechanisms
whereby different enzymes adjust their structures to
particular ends.
Acknowledgements
I thank C-I Br~ind6n for suggestions.
References and recommended reading
Papers of particular interest, published within the annual period of
review, have been highlighted as:
• of special interest
•" of outstanding interest
1. Adams MJ, Ford CG, Koekoek R, Lentz PJ Jr, McPherson A Jr,
Rossmann MG, Smiley IE, Schevitz RW, Wonacott AJ: Struc-
ture of lactate dehydrogenase at 2.8,~ resolution, Nature 1970,
227:1098-1103.
2. Brand~n CI, Zeppezauer E, Boiwe T, S6derlund G, Soderberg B-
O, Nordstrom B: X-ray studies of horse liver alcohol dehydro-
genase. In Pyridine Nucleotide-Dependent Dehydrogenases.
Edited by Sund H. Berlin: Springer-Verlag; 1970:129-134.
3. Rossmann MG: Molecular fossils. New Sci 1974, 31:266-268.
4. Rao ST, Rossmann MG: Comparison of super-secondary struc-
tures in proteins. J Mol Biol 1973, 76:241-256.
5. Brknd~n CI, Eklund H, Nordstrom B, Boiwe 1-, S6derlund G,
Zeppezauer E, Ohlsson I, Akeson A: Structure of liver alcohol
dehydrogenase at 2.9-,~ resolution. Proc Natl Acad Sci USA
1973, 70:2439-2442.
6. Rossmann MG, Moras D, Olsen KW: Chemical and biologi-
cal evolution of a nucleotide-binding protein. Nature 1974,
250:194-199.
7. Bernstein FC, Koetzle TF, Williams GJB, Meyer EE Jr, Brice MD,
Rodgers JR, Kennard O, Shimanouchi T, Tasumi M: The protein
databank: a computer-based archival file for macromolecular
structure. J Mol Biol 1977, 112:535-542.
8. Brenner SE, Chothia C, Hubbard TJP, Murzin AG: SCOP:
• a structural classification of proteins database for the in-
vestigation of sequences and structures. ] Mol Biol 1995,
247:536-540.
Description of hierarchical classification of proteins on the basis of fold-
ing pattern. Available over the World-Wide-Web. With the very large
number of structures now available, SCOP, or something like it, is a
necessary tool for research.

9. Brand~n Ch Relation between structure and function of cc/~-
proteins. Q Roy Biophys 1980, 13:317-338.
10. Wierenga RW, DeMaeyer MCH, Hol WGJ: Interaction of py-
rophosphate moieties with co-helices in dinucleotide-binding
proteins. Biochemistry 1985, 24:1346-1357.
11. Wierenga RW, Terpstra P, Hol WGJ: Prediction of the occur-
rence of the ADP-binding [[~c[3-foldin proteins, using an amino
acid sequence fingerprint. J Mol Biol 1986, 187:101-107.
12. Br;~nd~n CI, Tooze J: Introduction to Protein Structure. New
York: Garland Publishing Co; 1991:148-149.
13. Brenner SE, Chothia C, Hubbard TIP, Murzin AG: Understand-
* ing a protein's structure: using SCOP for fold interpretation.
Methods Enzymol 1996, 266:in press.
Description of the SCOP hierarchy of structural classification, and ap-
plication to NAD(P) binding proteins. This article describes parts of the
dehydrogenasedike structures outside the NAD-binding domains them-
selves, and lists molecules with other folds that bind NAD and related
ligands.
14. Eklund H, Samama I-P, Jones TA: Crystallographic in-
vestigations of nicotinamide adenine dinucleotide binding
to horse liver alcohol dehydrogenase. Biochemistry 1984,
2 3 : 5982-5996.
15. Dunn CR, Wilks HM, Halsall Dr, Atkinson T, Clarke AR, Muir-
head H, Holbrook Jr: Design and synthesis of new enzymes
based on the lactate dehydrogenase framework. Philos Trans
R 5oc Lond [Biol] 1991, 332:177-184.
16. Hall MD, Banaszak LJ: Crystal structure of a ternary complex
of Escherichia coil malale dehydrogenase, citrate and NAD at
1.9 angstroms resolution. J Mol Biol 1993, 232:213-222.
17. Skarzynski T, Moody PCE, Wonacott AJ: Structure of
holo-glyceraldehyde-3-phosphate dehydrogenase from Bacil-
lus stearothermophilus at 1.8,~ resolution. J Mol Biol 1987,
193:171-187.
N A D - b i n d i n g d o m a i n s of dehydrogenases Lesk 783
18. Phillips C, Gover S, Adams Mr: Structure of 6-phosphoglu-
• conate dehydrogenase refined at 2A resolution. Acta Crystal-
Iogr D 1995, 51:290-307.
Description of structure determination of sheep liver enzyme at 2,g, res-
olution. Contains detailed list of the structural role of residues conserved
in known 6-phosphogluconate dehydrogenase sequences.
19. Ghosh D, Weeks CM, Grochulski P, Duax WL, Erman M,
Rimsay RL, Orr JC: Three-dimensional structure of holo
3cc,20i3-hydroxysteroid dehydrogenase: a member of a short-
chain dehydrogenase family. Proc Nat/ Acad 5ci USA 1991,
88:10064-10068.
20. Varughese KI, Skinner MM, Whiteley JM, Matthews DA, Xuong
NH: Crystal structure of rat liver dihydropteridine reductase.
Proc Natl Acad Sci USA 1992, 89:6080-6084.
21. Lamzin VS, Aleshin AE, Strokopytov BV, Yukhnevich MG,
Popov VO, Harutyunyan EH, Wilson KS: Crystal structure of
NAD-dependent formate dehydrogenase. Eur I Biochem 1992,
206:441-452.
22. PerssonB, Krook M, Drnvall H: Characteristics of short-chain
alcohol dehydrogenases and related enzymes. Eur ] Biochem
1991, 200:537-543.
23. Edwards KJ, Thorn JM, Daniher JA, Dixon NE, Ollis DL: Crys-
• tallization and preliminary X-ray diffraction studies on a sol-
uble Escherichia coli quinone oxidoreductase. J Mol Biol 1994,
240:501-503.
A preliminary description of the structure determination.
24. Karplus PA, Daniels MH, Herriott JR: Atomic structure of
ferredoxin-NADP+ reductase: prototype for a structurally novel
flavoenzyme family. Science 1991, 251:60-66.
AM Lesk, l)epartment of Haematolog% University of Cambridge
Clinical School, MI~,C Centre, Hills Road, Cambridge CB2
2QH, UK.