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PDBsum entry 1gdh

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Oxidoreductase(choh (d)-NAD(p)+ (a)) PDB id
1gdh
Jmol
Contents
Protein chains
320 a.a. *
Ligands
SO4 ×2
Waters ×197
* Residue conservation analysis
PDB id:
1gdh
Name: Oxidoreductase(choh (d)-NAD(p)+ (a))
Title: Crystal structure of a NAD-dependent d-glycerate dehydrogenase at 2.4 angstroms resolution
Structure: D-glycerate dehydrogenase. Chain: a, b. Engineered: yes
Source: Hyphomicrobium methylovorum. Organism_taxid: 84
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.189    
Authors: J.D.Goldberg,T.Yoshida,P.Brick
Key ref:
J.D.Goldberg et al. (1994). Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. J Mol Biol, 236, 1123-1140. PubMed id: 8120891 DOI: 10.1016/0022-2836(94)90016-7
Date:
22-Sep-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36234  (DHGY_HYPME) -  Glycerate dehydrogenase
Seq:
Struc:
322 a.a.
320 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.29  - Glycerate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glycerate + NAD+ = hydroxypyruvate + NADH
D-glycerate
+ NAD(+)
= hydroxypyruvate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0022-2836(94)90016-7 J Mol Biol 236:1123-1140 (1994)
PubMed id: 8120891  
 
 
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
J.D.Goldberg, T.Yoshida, P.Brick.
 
  ABSTRACT  
 
D-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of hydroxypyruvate to D-glycerate. GDH is a member of a family of NAD-dependent dehydrogenases that is characterized by a specificity for the D-isomer of the hydroxyacid substrate. The crystal structure of the apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined by the method of isomorphous replacement and refined at 2.4 A resolution using a restrained least-squares method. The crystallographic R-factor is 19.4% for all 24,553 measured reflections between 10.0 and 2.4 A resolution. The GDH molecule is a symmetrical dimer composed of subunits of molecular mass 38,000, and shares significant structural homology with another NAD-dependent enzyme, formate dehydrogenase. The GDH subunit consists of two structurally similar domains that are approximately related to each other by 2-fold symmetry. The domains are separated by a deep cleft that forms the putative NAD and substrate binding sites. One of the domains has been identified as the NAD-binding domain based on its close structural similarity to the NAD-binding domains of other NAD-dependent dehydrogenases. The topology of the second domain is different from that found in the various catalytic domains of other dehydrogenases. A model of a ternary complex of GDH has been built in which putative catalytic residues are identified based on sequence homology between the D-isomer specific dehydrogenases. A structural comparison between GDH and L-lactate dehydrogenase indicates a convergence of active site residues and geometries for these two enzymes. The reactions catalyzed are chemically equivalent but of opposing stereospecificity. A hypothesis is presented to explain how the two enzymes may exploit the same coenzyme stereochemistry and a similar spatial arrangement of catalytic residues to carry out reactions that proceed to opposite enantiomers.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. .\ trrro iagram of the (:I)H holornzymr model intlic*ating the hypothetical juxtaposition of the SAD ~olrc~rtlr and protein srcontlar~ suc*turr rlemrnts.
Figure 9.
Figure 9. Stereo view showing the active ite of: a) D-glycerate ehydrogenase apoezyme: (b) D-glp?ratP ehydrogenase modelled ternary complex (only the nicotinamide ribose moiety of the coenzyme is shown): (c) I.-lactate ehydrogenase ternary complex with oxamate inhibitor (OXM). Co-ordinates are from dataset ILDM Protein Data Bak.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1994, 236, 1123-1140) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445235 V.Janiak, M.Petersen, M.Zentgraf, G.Klebe, and A.Heine (2010).
Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth.
  Acta Crystallogr D Biol Crystallogr, 66, 593-603.
PDB code: 3baz
  19342795 J.Domenech, P.J.Baker, S.E.Sedelnikova, H.F.Rodgers, D.W.Rice, and J.Ferrer (2009).
Crystallization and preliminary X-ray analysis of D-2-hydroxyacid dehydrogenase from Haloferax mediterranei.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 415-418.  
19727923 M.E.Cristescu, and E.E.Egbosimba (2009).
Evolutionary history of D-lactate dehydrogenases: a phylogenomic perspective on functional diversity in the FAD binding oxidoreductase/transferase type 4 family.
  J Mol Evol, 69, 276-287.  
18391442 Y.Wada, S.Iwai, Y.Tamura, T.Ando, T.Shinoda, K.Arai, and H.Taguchi (2008).
A new family of D-2-hydroxyacid dehydrogenases that comprises D-mandelate dehydrogenases and 2-ketopantoate reductases.
  Biosci Biotechnol Biochem, 72, 1087-1094.  
17928715 I.Saichana, Y.Ano, O.Adachi, K.Matsushita, and H.Toyama (2007).
Preparation of enzymes required for enzymatic quantification of 5-keto-D-gluconate and 2-keto-D-gluconate.
  Biosci Biotechnol Biochem, 71, 2478-2486.  
17142460 L.A.Pearson, K.D.Barrow, and B.A.Neilan (2007).
Characterization of the 2-hydroxy-acid dehydrogenase McyI, encoded within the microcystin biosynthesis gene cluster of Microcystis aeruginosa PCC7806.
  J Biol Chem, 282, 4681-4692.  
17327673 S.Yoshikawa, R.Arai, Y.Kinoshita, T.Uchikubo-Kamo, T.Wakamatsu, R.Akasaka, R.Masui, T.Terada, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2007).
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
  Acta Crystallogr D Biol Crystallogr, 63, 357-365.
PDB codes: 2dbq 2dbr 2dbz
15634349 B.M.Martins, S.Macedo-Ribeiro, J.Bresser, W.Buckel, and A.Messerschmidt (2005).
Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans.
  FEBS J, 272, 269-281.
PDB code: 1xdw
16233829 H.Muramatsu, H.Mihara, M.Goto, I.Miyahara, K.Hirotsu, T.Kurihara, and N.Esaki (2005).
A new family of NAD(P)H-dependent oxidoreductases distinct from conventional Rossmann-fold proteins.
  J Biosci Bioeng, 99, 541-547.  
15668249 S.Dey, G.A.Grant, and J.C.Sacchettini (2005).
Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits.
  J Biol Chem, 280, 14892-14899.
PDB code: 1ygy
15734738 T.Shinoda, K.Arai, M.Shigematsu-Iida, Y.Ishikura, S.Tanaka, T.Yamada, M.S.Kimber, E.F.Pai, S.Fushinobu, and H.Taguchi (2005).
Distinct conformation-mediated functions of an active site loop in the catalytic reactions of NAD-dependent D-lactate dehydrogenase and formate dehydrogenase.
  J Biol Chem, 280, 17068-17075.  
15206932 V.Ali, T.Hashimoto, Y.Shigeta, and T.Nozaki (2004).
Molecular and biochemical characterization of D-phosphoglycerate dehydrogenase from Entamoeba histolytica. A unique enteric protozoan parasite that possesses both phosphorylated and nonphosphorylated serine metabolic pathways.
  Eur J Biochem, 271, 2670-2681.  
12897026 C.Tokuda, Y.Ishikura, M.Shigematsu, H.Mutoh, S.Tsuzuki, Y.Nakahira, Y.Tamura, T.Shinoda, K.Arai, O.Takahashi, and H.Taguchi (2003).
Conversion of Lactobacillus pentosus D-lactate dehydrogenase to a D-hydroxyisocaproate dehydrogenase through a single amino acid replacement.
  J Bacteriol, 185, 5023-5026.  
12805226 M.Nardini, S.Spanò, C.Cericola, A.Pesce, A.Massaro, E.Millo, A.Luini, D.Corda, and M.Bolognesi (2003).
CtBP/BARS: a dual-function protein involved in transcription co-repression and Golgi membrane fission.
  EMBO J, 22, 3122-3130.
PDB codes: 1hku 1hl3
14529270 R.Woodyer, W.A.van der Donk, and H.Zhao (2003).
Relaxing the nicotinamide cofactor specificity of phosphite dehydrogenase by rational design.
  Biochemistry, 42, 11604-11614.  
12419215 C.W.Carter, and W.L.Duax (2002).
Did tRNA synthetase classes arise on opposite strands of the same gene?
  Mol Cell, 10, 705-708.  
12199695 J.K.Bell, P.J.Pease, J.E.Bell, G.A.Grant, and L.J.Banaszak (2002).
De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal.
  Eur J Biochem, 269, 4176-4184.  
11910018 M.R.Chance, A.R.Bresnick, S.K.Burley, J.S.Jiang, C.D.Lima, A.Sali, S.C.Almo, J.B.Bonanno, J.A.Buglino, S.Boulton, H.Chen, N.Eswar, G.He, R.Huang, V.Ilyin, L.McMahan, U.Pieper, S.Ray, M.Vidal, and L.K.Wang (2002).
Structural genomics: a pipeline for providing structures for the biologist.
  Protein Sci, 11, 723-738.
PDB code: 1jr7
12419229 V.Kumar, J.E.Carlson, K.A.Ohgi, T.A.Edwards, D.W.Rose, C.R.Escalante, M.G.Rosenfeld, and A.K.Aggarwal (2002).
Transcription corepressor CtBP is an NAD(+)-regulated dehydrogenase.
  Mol Cell, 10, 857-869.
PDB code: 1mx3
11823242 Y.Tamura, A.Ohkubo, S.Iwai, Y.Wada, T.Shinoda, K.Arai, S.Mineki, M.Iida, and H.Taguchi (2002).
Two forms of NAD-dependent D-mandelate dehydrogenase in Enterococcus faecalis IAM 10071.
  Appl Environ Microbiol, 68, 947-951.  
11163272 F.Schmitz, A.Königstorfer, and T.C.Südhof (2000).
RIBEYE, a component of synaptic ribbons: a protein's journey through evolution provides insight into synaptic ribbon function.
  Neuron, 28, 857-872.  
10712593 S.Kochhar, V.S.Lamzin, A.Razeto, M.Delley, H.Hottinger, and J.E.Germond (2000).
Roles of his205, his296, his303 and Asp259 in catalysis by NAD+-specific D-lactate dehydrogenase.
  Eur J Biochem, 267, 1633-1639.  
  10388723 A.E.Hayford, A.Petersen, F.K.Vogensen, and M.Jakobsen (1999).
Use of conserved randomly amplified polymorphic DNA (RAPD) fragments and RAPD pattern for characterization of Lactobacillus fermentum in Ghanaian fermented maize dough.
  Appl Environ Microbiol, 65, 3213-3221.  
10477256 Y.Xu, G.Bhargava, H.Wu, G.Loeber, and L.Tong (1999).
Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme: a new class of oxidative decarboxylases.
  Structure, 7, R877-R889.  
9724649 J.Turner, and M.Crossley (1998).
Cloning and characterization of mCtBP2, a co-repressor that associates with basic Krüppel-like factor and other mammalian transcriptional regulators.
  EMBO J, 17, 5129-5140.  
9665174 K.L.Britton, Y.Asano, and D.W.Rice (1998).
Crystal structure and active site location of N-(1-D-carboxylethyl)-L-norvaline dehydrogenase.
  Nat Struct Biol, 5, 593-601.
PDB code: 1bg6
9586999 M.A.Turner, C.S.Yuan, R.T.Borchardt, M.S.Hershfield, G.D.Smith, and P.L.Howell (1998).
Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
  Nat Struct Biol, 5, 369-376.
PDB code: 1a7a
9665169 P.J.Baker, Y.Sawa, H.Shibata, S.E.Sedelnikova, and D.W.Rice (1998).
Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.
  Nat Struct Biol, 5, 561-567.
PDB codes: 1pjb 1pjc 1say
  9605319 V.S.Stoll, A.V.Manohar, W.Gillon, E.L.MacFarlane, R.C.Hynes, and E.F.Pai (1998).
A thioredoxin fusion protein of VanH, a D-lactate dehydrogenase from Enterococcus faecium: cloning, expression, purification, kinetic analysis, and crystallization.
  Protein Sci, 7, 1147-1155.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9013553 B.X.Yan, and Y.Q.Sun (1997).
Glycine residues provide flexibility for enzyme active sites.
  J Biol Chem, 272, 3190-3194.  
9063466 N.Bernard, K.Johnsen, J.L.Gelpi, J.A.Alvarez, T.Ferain, D.Garmyn, P.Hols, A.Cortes, A.R.Clarke, J.J.Holbrook, and J.Delcour (1997).
D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus. II. Mutagenic analysis of catalytically important residues.
  Eur J Biochem, 244, 213-219.  
  8771194 G.A.Grant, D.J.Schuller, and L.J.Banaszak (1996).
A model for the regulation of D-3-phosphoglycerate dehydrogenase, a Vmax-type allosteric enzyme.
  Protein Sci, 5, 34-41.  
8740366 V.S.Stoll, M.S.Kimber, and E.F.Pai (1996).
Insights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase.
  Structure, 4, 437-447.  
7567953 C.Vinals, X.De Bolle, E.Depiereux, and E.Feytmans (1995).
Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.
  Proteins, 21, 307-318.  
  7539419 D.Garmyn, T.Ferain, N.Bernard, P.Hols, B.Delplace, and J.Delcour (1995).
Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis.
  J Bacteriol, 177, 3427-3437.  
7719856 D.J.Schuller, G.A.Grant, and L.J.Banaszak (1995).
The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
  Nat Struct Biol, 2, 69-76.
PDB code: 1psd
7479821 U.Schaeper, J.M.Boyd, S.Verma, E.Uhlmann, T.Subramanian, and G.Chinnadurai (1995).
Molecular cloning and characterization of a cellular phosphoprotein that interacts with a conserved C-terminal domain of adenovirus E1A involved in negative modulation of oncogenic transformation.
  Proc Natl Acad Sci U S A, 92, 10467-10471.  
8749373 V.S.Lamzin, Z.Dauter, and K.S.Wilson (1995).
How nature deals with stereoisomers.
  Curr Opin Struct Biol, 5, 830-836.  
8055948 T.Yoshida, K.Yamaguchi, T.Hagishita, T.Mitsunaga, A.Miyata, T.Tanabe, H.Toh, T.Ohshiro, M.Shimao, and Y.Izumi (1994).
Cloning and expression of the gene for hydroxypyruvate reductase (D-glycerate dehydrogenase from an obligate methylotroph Hyphomicrobium methylovorum GM2.
  Eur J Biochem, 223, 727-732.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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