PDBsum entry 1zji

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
257 a.a. *
2PG ×2
_CD ×2
Waters ×111
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Aquifex aeolicus kdo8ps r106g mutant in complex with 2pga an
Structure: 2-dehydro-3-deoxyphosphooctonate aldolase. Chain: a, b. Synonym: phospho-2-dehydro-3-deoxyoctonate aldolase, 3-deox octulosonic acid 8-phosphate synthetase, kdo-8-phosphate sy kdo 8-p synthase, kdops. Engineered: yes. Mutation: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: kdsa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
2.25Å     R-factor:   0.203     R-free:   0.242
Authors: X.Xu,F.Kona,J.Wang,J.Lu,T.Stemmler,D.L.Gatti
Key ref:
X.Xu et al. (2005). The catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase: role of the L7 loop. Biochemistry, 44, 12434-12444. PubMed id: 16156656 DOI: 10.1021/bi051095q
28-Apr-05     Release date:   27-Sep-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O66496  (KDSA_AQUAE) -  2-dehydro-3-deoxyphosphooctonate aldolase
267 a.a.
257 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - 3-deoxy-8-phosphooctulonate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 2-dehydro-3- deoxy-D-octonate 8-phosphate + phosphate
Bound ligand (Het Group name = 2PG)
matches with 90.91% similarity
D-arabinose 5-phosphate
Bound ligand (Het Group name = R5P)
corresponds exactly
+ H(2)O
= 2-dehydro-3- deoxy-D-octonate 8-phosphate
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  


DOI no: 10.1021/bi051095q Biochemistry 44:12434-12444 (2005)
PubMed id: 16156656  
The catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase: role of the L7 loop.
X.Xu, F.Kona, J.Wang, J.Lu, T.Stemmler, D.L.Gatti.
KDO8P synthase catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form the 8-carbon sugar KDO8P and inorganic phosphate (P(i)). The X-ray structure of the wild-type enzyme shows that when both PEP and A5P bind, the active site becomes isolated from the environment due to a conformational change of the L7 loop. The structures of the R106G mutant, without substrates, and with PEP and PEP plus A5P bound, were determined and reveal that in R106G closure of the L7 loop is impaired. The structural perturbations originating from the loss of the Arg(106) side chain point to a role of the L2 loop in stabilizing the closed conformation of the L7 loop. Despite the increased exposure of the R106G active site, no abnormal reaction of PEP with water was observed, ruling out the hypothesis that the primary function of the L7 loop is to shield the active site from bulk solvent during the condensation reaction. However, the R106G enzyme displays several kinetic abnormalities on both the substrate side (smaller K(m)(PEP), larger K(i)(A5P) and K(m)(A5P)) and the product side (smaller K(i)(Pi) and K(i)(KDO8P)) of the reaction. As a consequence, the mutant enzyme is less severely inhibited by A5P and more severely inhibited by P(i) and KDO8P. Simulations of the flux of KDO8P synthesis under metabolic steady-state conditions (constant concentration of reactants and products over time) suggest that in vivo R106G is expected to perform optimally in a narrower range of substrate and product concentrations than the wild-type enzyme.