PDBsum entry 1ky8

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Oxidoreductase PDB id
Protein chain
499 a.a. *
Waters ×386
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of the non-phosphorylating glyceraldehyde- phosphate dehydrogenase
Structure: Glyceraldehyde-3-phosphate dehydrogenase. Chain: a. Synonym: NADP+. Engineered: yes
Source: Thermoproteus tenax. Organism_taxid: 2271. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
2.40Å     R-factor:   0.208     R-free:   0.242
Authors: E.Pohl,N.Brunner,M.Wilmanns,R.Hensel
Key ref:
E.Pohl et al. (2002). The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax. J Biol Chem, 277, 19938-19945. PubMed id: 11842090 DOI: 10.1074/jbc.M112244200
04-Feb-02     Release date:   04-Feb-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O57693  (O57693_THETE) -  NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
501 a.a.
499 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate + NADP+ + H2O = 3-phospho-D-glycerate + NADPH
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = NAP)
corresponds exactly
+ H(2)O
= 3-phospho-D-glycerate
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     catalytic activity     7 terms  


DOI no: 10.1074/jbc.M112244200 J Biol Chem 277:19938-19945 (2002)
PubMed id: 11842090  
The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax.
E.Pohl, N.Brunner, M.Wilmanns, R.Hensel.
The NAD(+)-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from the hyperthermophilic archaeum Thermoproteus tenax represents an archaeal member of the diverse superfamily of aldehyde dehydrogenases (ALDHs). GAPN catalyzes the irreversible oxidation of d-glyceraldehyde 3-phosphate to 3-phosphoglycerate. In this study, we present the crystal structure of GAPN in complex with its natural inhibitor NADP(+) determined by multiple anomalous diffraction methods. The structure was refined to a resolution of 2.4 A with an R-factor of 0.21. The overall fold of GAPN is similar to the structures of ALDHs described previously, consisting of three domains: a nucleotide-binding domain, a catalytic domain, and an oligomerization domain. Local differences in the active site are responsible for substrate specificity. The inhibitor NADP(+) binds at an equivalent site to the cosubstrate-binding site of other ALDHs and blocks the enzyme in its inactive state, possibly preventing the transition to the active conformation. Structural comparison between GAPN from the hyperthermophilic T. tenax and homologs of mesophilic organisms establishes several characteristics of thermostabilization. These include protection against heat-induced covalent modifications by reducing and stabilizing labile residues, a decrease in number and volume of empty cavities, an increase in beta-strand content, and a strengthening of subunit contacts by ionic and hydrophobic interactions.
  Selected figure(s)  
Figure 3.
Fig. 3. Least-squares superposition of structurally equivalent C^ atoms of Tt-GAPN (red) and Sm-GAPN (blue) (10).
Figure 4.
Fig. 4. a, stereo view of a representative portion of the experimental electron density map after solvent flattening at a 1.5- level showing the inhibitor-binding site. The final model of NADP+ is superimposed as a ball-and-stick representation. b, close-up stereo view of the binding site showing the hydrogen bonds between the phosphate and protein atoms. The nicotinamide moiety has been omitted for clarity. c, position of NADP+ in the structures of Tt-GAPN ( gray bonds) and Sm-GAPN (white bonds) after the least-squares superposition of the C^ trace of the two enzymes.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 19938-19945) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18848533 S.A.Krupenko (2009).
FDH: an aldehyde dehydrogenase fusion enzyme in folate metabolism.
  Chem Biol Interact, 178, 84-93.  
18186475 A.Pauluhn, H.Ahmed, E.Lorentzen, S.Buchinger, D.Schomburg, B.Siebers, and E.Pohl (2008).
Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax.
  Proteins, 72, 35-43.
PDB codes: 2r91 2r94
18218709 J.S.Rodríguez-Zavala (2008).
Enhancement of coenzyme binding by a single point mutation at the coenzyme binding domain of E. coli lactaldehyde dehydrogenase.
  Protein Sci, 17, 563-570.  
17549431 T.J.Ettema, H.Ahmed, A.C.Geerling, J.van der Oost, and B.Siebers (2008).
The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway.
  Extremophiles, 12, 75-88.  
17573704 A.Mura, F.Pintus, R.Medda, G.Floris, A.C.Rinaldi, and A.Padiglia (2007).
Catalase and antiquitin from Euphorbia characias: two proteins involved in plant defense?
  Biochemistry (Mosc), 72, 501-508.  
17619949 L.Fourrat, A.Iddar, F.Valverde, A.Serrano, and A.Soukri (2007).
Cloning, gene expression and characterization of a novel bacterial NAD-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Neisseria meningitidis strain Z2491.
  Mol Cell Biochem, 305, 209-219.  
16256419 B.Siebers, and P.Schönheit (2005).
Unusual pathways and enzymes of central carbohydrate metabolism in Archaea.
  Curr Opin Microbiol, 8, 695-705.  
15028704 B.Siebers, B.Tjaden, K.Michalke, C.Dörr, H.Ahmed, M.Zaparty, P.Gordon, C.W.Sensen, A.Zibat, H.P.Klenk, S.C.Schuster, and R.Hensel (2004).
Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data.
  J Bacteriol, 186, 2179-2194.  
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.