PDBsum entry 1q6l

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
214 a.a. *
TX4 ×2
_MG ×2
Waters ×319
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound l-threonohydroxamate 4-phosphate
Structure: 3-keto-l-gulonate 6-phosphate decarboxylase. Chain: a, b. Synonym: probable hexulose-6-phosphate synthase. Humps. D- arabino 3-hexulose 6-phosphate formaldehyde lyase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.175     R-free:   0.218
Authors: E.L.Wise,W.S.Yew,J.A.Gerlt,I.Rayment
Key ref:
E.L.Wise et al. (2003). Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily. Biochemistry, 42, 12133-12142. PubMed id: 14567674 DOI: 10.1021/bi0348819
13-Aug-03     Release date:   28-Oct-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P39304  (ULAD_ECOLI) -  3-keto-L-gulonate-6-phosphate decarboxylase UlaD
216 a.a.
214 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 3-dehydro-L-gulonate-6-phosphate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 3-dehydro-L-gulonate 6-phosphate = L-xylulose 5-phosphate + CO2
3-dehydro-L-gulonate 6-phosphate
L-xylulose 5-phosphate
Bound ligand (Het Group name = TX4)
matches with 75.00% similarity
+ CO(2)
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1021/bi0348819 Biochemistry 42:12133-12142 (2003)
PubMed id: 14567674  
Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.
E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment.
3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20938979 I.Orita, A.Kita, H.Yurimoto, N.Kato, Y.Sakai, and K.Miki (2010).
Crystal structure of 3-hexulose-6-phosphate synthase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.
  Proteins, 78, 3488-3492.
PDB code: 3ajx
18849419 R.Shi, M.Pineda, E.Ajamian, Q.Cui, A.Matte, and M.Cygler (2008).
Structure of L-xylulose-5-Phosphate 3-epimerase (UlaE) from the anaerobic L-ascorbate utilization pathway of Escherichia coli: identification of a novel phosphate binding motif within a TIM barrel fold.
  J Bacteriol, 190, 8137-8144.
PDB codes: 3cqh 3cqi 3cqj 3cqk
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