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PDBsum entry 1x0v

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1x0v
Jmol
Contents
Protein chain
348 a.a. *
Ligands
SO4 ×14
Waters ×651
* Residue conservation analysis
PDB id:
1x0v
Name: Oxidoreductase
Title: Crystal structure of homo sapien glycerol-3-phosphate dehydrogenase 1
Structure: Glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic. Chain: a, b. Synonym: gpd-c, gpdh-c. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.205     R-free:   0.249
Authors: Z.Rao,X.Ou
Key ref:
X.Ou et al. (2006). Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1). J Mol Biol, 357, 858-869. PubMed id: 16460752 DOI: 10.1016/j.jmb.2005.12.074
Date:
30-Mar-05     Release date:   11-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P21695  (GPDA_HUMAN) -  Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
Seq:
Struc:
349 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.8  - Glycerol-3-phosphate dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH
sn-glycerol 3-phosphate
+ NAD(+)
= glycerone phosphate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     small molecule metabolic process   18 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.12.074 J Mol Biol 357:858-869 (2006)
PubMed id: 16460752  
 
 
Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1).
X.Ou, C.Ji, X.Han, X.Zhao, X.Li, Y.Mao, L.L.Wong, M.Bartlam, Z.Rao.
 
  ABSTRACT  
 
Homo sapiensl-alpha-glycerol-3-phosphate dehydrogenase 1 (GPD1) catalyzes the reversible biological conversion of dihydroxyacetone (DHAP) to glycerol-3-phosphate. The GPD1 protein was expressed in Escherichia coli, and purified as a fusion protein with glutathione S-transferase. Here we report the apoenzyme structure of GPD1 determined by multiwavelength anomalous diffraction phasing, and other complex structures with small molecules (NAD(+) and DHAP) by the molecular replacement method. This enzyme structure is organized into two distinct domains, the N-terminal eight-stranded beta-sheet sandwich domain and the C-terminal helical substrate-binding domain. An electrophilic catalytic mechanism by the epsilon-NH(3)(+) group of Lys204 is proposed on the basis of the structural analyses. In addition, the inhibitory effects of zinc and sulfate on GPDHs are assayed and discussed.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The putative active site. The phosphate group of DHAP is half-encircled by the side-chain of Arg269, and interacts with Arg269 and Gly268 directly by hydrogen bonds (not shown). The conserved residues Lys204, Asn205, Asp260 and Thr264 form a stable hydrogen bonding network. The other hydrogen bonding network includes residues Lys120 and Asp260, as well as an ordered water molecule (with a B-factor of 16.4 Å2) which hydrogen bonds to Gly149 and Asn151 (not shown). In these two electrostatic networks, only the e-NH3+ group of Lys204 is the nearest to the C[2] atom of DHAP (3.4 Å).
Figure 7.
Figure 7. (a) and (b) Superposition of the human GPD1 apoenzyme structure (red) with the L. mexicana GPDH structures in complex with NAD (blue, PDB code: 1EVZ), and in complex with both NAD and DHAP (green, PDB code: 1N1E). (b) An enlarged image of the shaded area in (a). The structure of human apo-GPD1 is structurally closer to the 1N1E structure (closed form) of L. mexicana than the 1EVZ structure (open form) of L. mexicana.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 858-869) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20857217 Y.Z.Gao, Y.Jiang, X.Wu, C.Y.Bai, Y.C.Pan, and Y.Z.Sun (2011).
Molecular characteristics and expression profiles of glycerol-3-phosphate dehydrogenase 1 (GPD1) gene in pig.
  Mol Biol Rep, 38, 1875-1881.  
20026609 S.Jung, M.Marelli, R.A.Rachubinski, D.R.Goodlett, and J.D.Aitchison (2010).
Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress.
  J Biol Chem, 285, 6739-6749.  
20304913 W.Shen, J.Q.Li, M.Dauk, Y.Huang, C.Periappuram, Y.Wei, and J.Zou (2010).
Metabolic and transcriptional responses of glycerolipid pathways to a perturbation of glycerol 3-phosphate metabolism in Arabidopsis.
  J Biol Chem, 285, 22957-22965.  
19666841 C.R.Valdivia, K.Ueda, M.J.Ackerman, and J.C.Makielski (2009).
GPD1L links redox state to cardiac excitability by PKC-dependent phosphorylation of the sodium channel SCN5A.
  Am J Physiol Heart Circ Physiol, 297, H1446-H1452.  
19618917 K.Toth, T.L.Amyes, B.M.Wood, K.K.Chan, J.A.Gerlt, and J.P.Richard (2009).
An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms.
  Biochemistry, 48, 8006-8013.  
19551475 Y.He, X.Meng, Q.Fan, X.Sun, Z.Xu, and R.Song (2009).
Cloning and characterization of two novel chloroplastic glycerol-3-phosphate dehydrogenases from Dunaliella viridis.
  Plant Mol Biol, 71, 193-205.  
18296637 J.I.Yeh, U.Chinte, and S.Du (2008).
Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
  Proc Natl Acad Sci U S A, 105, 3280-3285.
PDB codes: 2qcu 2r45 2r46 2r4e 2r4j
18293941 J.R.Morrow, T.L.Amyes, and J.P.Richard (2008).
Phosphate binding energy and catalysis by small and large molecules.
  Acc Chem Res, 41, 539-548.  
18376850 W.Y.Tsang, T.L.Amyes, and J.P.Richard (2008).
A substrate in pieces: allosteric activation of glycerol 3-phosphate dehydrogenase (NAD+) by phosphite dianion.
  Biochemistry, 47, 4575-4582.  
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 codes are shown on the right.