PDBsum entry 1bwz

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protein links
Isomerase PDB id
Protein chain
274 a.a. *
Waters ×29
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Diaminopimelate epimerase from hemophilus influenzae
Structure: Protein (diaminopimelate epimerase). Chain: a. Synonym: dap epimerase. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Gene: dapf. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.72Å     R-factor:   0.190     R-free:   0.242
Authors: M.Cirilli,R.Zheng,G.Scapin,J.S.Blanchard
Key ref:
M.Cirilli et al. (1998). Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase. Biochemistry, 37, 16452-16458. PubMed id: 9843410 DOI: 10.1021/bi982138o
29-Sep-98     Release date:   16-Dec-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P44859  (DAPF_HAEIN) -  Diaminopimelate epimerase
274 a.a.
274 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.  - Diaminopimelate epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Lysine biosynthesis (later stages)
      Reaction: LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
= meso-diaminoheptanedioate
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     cellular amino acid biosynthetic process   3 terms 
  Biochemical function     isomerase activity     2 terms  


    Added reference    
DOI no: 10.1021/bi982138o Biochemistry 37:16452-16458 (1998)
PubMed id: 9843410  
Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.
M.Cirilli, R.Zheng, G.Scapin, J.S.Blanchard.
The Haemophilus influenzae diaminopimelate epimerase was cloned, expressed, purified, and crystallized in the C2221 space group (a = 102.1 A, b = 115.4 A, c = 66.3 A, alpha = beta = gamma = 90 degrees). The three-dimensional structure was solved to 2.7 A using a single Pt derivative and the Se-Met-substituted enzyme to a conventional R factor of 19.0% (Rfree = 24.2%). The 274 amino acid enzyme consists of two structurally homologous domains, each containing eight beta-strands and two alpha-helices. Diaminopimelate epimerase is a representative of the PLP-independent amino acid racemases, for which no structure has yet been determined and substantial evidence exists supporting the role of two cysteine residues as the catalytic acid and base. Cys73 of the amino terminal domain is found in disulfide linkage, at the domain interface, with Cys217 of the carboxy terminal domain, and we suggest that these two cysteine residues in the reduced, active enzyme function as the acid and base in the mechanism.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20564572 D.Matsui, and T.Oikawa (2010).
Detection and function of the intramolecular disulfide bond in arginine racemase: an enzyme with broad substrate specificity.
  Chem Biodivers, 7, 1591-1602.  
19307721 V.Usha, L.G.Dover, D.I.Roper, K.Fütterer, and G.S.Besra (2009).
Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis.
  Acta Crystallogr D Biol Crystallogr, 65, 383-387.
PDB code: 3fve
18269631 V.Usha, L.G.Dover, D.L.Roper, and G.S.Besra (2008).
Characterization of Mycobacterium tuberculosis diaminopimelic acid epimerase: paired cysteine residues are crucial for racemization.
  FEMS Microbiol Lett, 280, 57-63.  
17669425 B.Nocek, E.Evdokimova, M.Proudfoot, M.Kudritska, L.L.Grochowski, R.H.White, A.Savchenko, A.F.Yakunin, A.Edwards, and A.Joachimiak (2007).
Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.
  J Mol Biol, 372, 456-469.
PDB codes: 2g9i 2phn
17579770 C.A.Hutton, M.A.Perugini, and J.A.Gerrard (2007).
Inhibition of lysine biosynthesis: an evolving antibiotic strategy.
  Mol Biosyst, 3, 458-465.  
17567742 G.S.Garvey, C.J.Rocco, J.C.Escalante-Semerena, and I.Rayment (2007).
The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function.
  Protein Sci, 16, 1274-1284.
PDB codes: 2pvz 2pw0
16446443 A.Buschiazzo, M.Goytia, F.Schaeffer, W.Degrave, W.Shepard, C.Grégoire, N.Chamond, A.Cosson, A.Berneman, N.Coatnoan, P.M.Alzari, and P.Minoprio (2006).
Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.
  Proc Natl Acad Sci U S A, 103, 1705-1710.
PDB codes: 1w61 1w62
16723397 B.Pillai, M.M.Cherney, C.M.Diaper, A.Sutherland, J.S.Blanchard, J.C.Vederas, and M.N.James (2006).
Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target.
  Proc Natl Acad Sci U S A, 103, 8668-8673.
PDB codes: 2gke 2gkj
  16754977 P.Herde, and W.Blankenfeldt (2006).
The purification, crystallization and preliminary structural characterization of human MAWDBP, a member of the phenazine biosynthesis-like protein family.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 546-549.  
17132860 S.Martínez-Rodríguez, M.Andújar-Sánchez, J.L.Neira, J.M.Clemente-Jiménez, V.Jara-Pérez, F.Rodríguez-Vico, and F.J.Las Heras-Vázquez (2006).
Site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from Sinorhizobium meliloti.
  Protein Sci, 15, 2729-2738.  
16327902 C.M.Diaper, A.Sutherland, B.Pillai, M.N.James, P.Semchuk, J.S.Blanchard, and J.C.Vederas (2005).
The stereoselective synthesis of aziridine analogues of diaminopimelic acid (DAP) and their interaction with dap epimerase.
  Org Biomol Chem, 3, 4402-4411.  
16021630 D.Liger, S.Quevillon-Cheruel, I.Sorel, M.Bremang, K.Blondeau, I.Aboulfath, J.Janin, H.van Tilbeurgh, and N.Leulliot (2005).
Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
  Proteins, 60, 778-786.
PDB code: 1ym5
15937278 H.Cheng, and N.V.Grishin (2005).
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
  Protein Sci, 14, 1902-1910.  
  16510993 K.S.Lee, S.M.Park, K.Y.Hwang, and Y.M.Chi (2005).
Crystallization and preliminary X-ray crystallographic studies of glutamate racemase from Lactobacillus fermenti.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 199-201.  
15103639 A.Grassick, G.Sulzenbacher, V.Roig-Zamboni, V.Campanacci, C.Cambillau, and Y.Bourne (2004).
Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase.
  Proteins, 55, 764-767.
PDB codes: 1qy9 1qya
14747737 A.J.Lloyd, T.Huyton, J.Turkenburg, and D.I.Roper (2004).
Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis.
  Acta Crystallogr D Biol Crystallogr, 60, 397-400.
PDB code: 1gqz
15545603 W.Blankenfeldt, A.P.Kuzin, T.Skarina, Y.Korniyenko, L.Tong, P.Bayer, P.Janning, L.S.Thomashow, and D.V.Mavrodi (2004).
Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.
  Proc Natl Acad Sci U S A, 101, 16431-16436.
PDB codes: 1sdj 1u1v 1u1w 1u1x 1xua 1xub
11342032 A.M.Paiva, D.E.Vanderwall, J.S.Blanchard, J.W.Kozarich, J.M.Williamson, and T.M.Kelly (2001).
Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis.
  Biochim Biophys Acta, 1545, 67-77.  
11738171 J.P.Richard, and T.L.Amyes (2001).
Proton transfer at carbon.
  Curr Opin Chem Biol, 5, 626-633.  
11679741 L.Liu, K.Iwata, Y.Kawarabayasi, H.Kikuchi, A.Kita, M.Yohda, and K.Miki (2001).
Crystallization and preliminary X-ray analysis of aspartate racemase from Pyrococcus horikoshii OT3.
  Acta Crystallogr D Biol Crystallogr, 57, 1674-1676.  
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
11371180 S.Glavas, and M.E.Tanner (2001).
Active site residues of glutamate racemase.
  Biochemistry, 40, 6199-6204.  
10508663 T.L.Born, and J.S.Blanchard (1999).
Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis.
  Curr Opin Chem Biol, 3, 607-613.  
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 code is shown on the right.