PDBsum entry 1jpm

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Isomerase PDB id
Protein chains
359 a.a. *
_MG ×4
Waters ×520
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: L-ala-d/l-glu epimerase
Structure: L-ala-d/l-glu epimerase. Chain: a, b, c, d. Fragment: l-ala-d/l-glu epimerase. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: ykfb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Octamer (from PQS)
2.25Å     R-factor:   0.197     R-free:   0.224
Authors: A.M.Gulick,D.M.Z.Schmidt,J.A.Gerlt,I.Rayment
Key ref:
A.M.Gulick et al. (2001). Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Biochemistry, 40, 15716-15724. PubMed id: 11747448 DOI: 10.1021/bi011641p
02-Aug-01     Release date:   21-Dec-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O34508  (AEEP_BACSU) -  L-Ala-D/L-Glu epimerase
366 a.a.
359 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.1.1  - Lysine racemase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-lysine = D-lysine
= D-lysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     4 terms  


    Added reference    
DOI no: 10.1021/bi011641p Biochemistry 40:15716-15724 (2001)
PubMed id: 11747448  
Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis.
A.M.Gulick, D.M.Schmidt, J.A.Gerlt, I.Rayment.
The members of the enolase superfamily catalyze different overall reactions, yet share a partial reaction that involves Mg(2+)-assisted enolization of the substrate carboxylate anion. The fate of the resulting enolate intermediate is determined by the active site of each enzyme. Several members of this superfamily have been structurally characterized to permit an understanding of the evolutionary strategy for using a common structural motif to catalyze different overall reactions. In the preceding paper, two new members of the superfamily were identified that catalyze the epimerization of the glutamate residue in L-Ala-D/L-Glu. These enzymes belong to the muconate lactonizing enzyme subgroup of the enolase superfamily, and their sequences are only 31% identical. The structure of YcjG, the epimerase from Escherichia coli, was determined by MAD phasing using both the SeMet-labeled protein and a heavy atom derivative. The structure of YkfB, the epimerase from Bacillus subtilis, was determined by molecular replacement using the muconate lactonizing enzyme as a search model. In this paper, we report the three-dimensional structures of these enzymes and compare them to the structure of o-succinylbenzoate synthase, another member of the muconate lactonizing enzyme subgroup.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18754693 J.F.Rakus, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, B.K.Hubbard, J.D.Delli, P.C.Babbitt, S.C.Almo, and J.A.Gerlt (2008).
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
  Biochemistry, 47, 9944-9954.
PDB codes: 2i5q 3box 3cxo
18535144 J.T.Park, and T.Uehara (2008).
How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan).
  Microbiol Mol Biol Rev, 72, 211.  
17932934 S.Wong, and M.P.Jacobson (2008).
Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins, 71, 153-164.  
17603539 L.Song, C.Kalyanaraman, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, S.Brown, H.J.Imker, P.C.Babbitt, S.C.Almo, M.P.Jacobson, and J.A.Gerlt (2007).
Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
  Nat Chem Biol, 3, 486-491.
PDB codes: 2p88 2p8b 2p8c
16049725 E.Rodríguez, F.Romarís, S.Lorenzo, J.Moreno, P.Bonay, F.M.Ubeira, and T.Gárate (2006).
A recombinant enolase from Anisakis simplex is differentially recognized in natural human and mouse experimental infections.
  Med Microbiol Immunol, 195, 1.  
17047777 Y.Terao, K.Miyamoto, and H.Ohta (2006).
Introduction of single mutation changes arylmalonate decarboxylase to racemase.
  Chem Commun (Camb), (), 3600-3602.  
16283547 W.Liu, W.Ye, Z.Wang, H.Chao, and J.Lian (2005).
Preparation and characterization of a truncated caricain lacking 41 residues from the N-terminal.
  Protein J, 24, 243-251.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12874381 A.M.Mulichak, H.C.Losey, W.Lu, Z.Wawrzak, C.T.Walsh, and R.M.Garavito (2003).
Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway.
  Proc Natl Acad Sci U S A, 100, 9238-9243.
PDB codes: 1pn3 1pnv
12055621 T.A.Keating, C.G.Marshall, C.T.Walsh, and A.E.Keating (2002).
The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains.
  Nat Struct Biol, 9, 522-526.
PDB code: 1l5a
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