DB code: D00454

CATH domain 3.10.310.10 : Diaminopimelate Epimerase; Chain A, domain 1 Catalytic domain
3.10.310.10 : Diaminopimelate Epimerase; Chain A, domain 1 Catalytic domain
E.C. 5.1.1.7
CSA 1bwz
M-CSA 1bwz
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P44859 Diaminopimelate epimerase
DAP epimerase
EC 5.1.1.7
NP_438909.1 (Protein)
NC_000907.1 (DNA/RNA sequence)
PF01678 (DAP_epimerase)
[Graphical View]

KEGG enzyme name
diaminopimelate epimerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P44859 DAPF_HAEIN LL-2,6-diaminoheptanedioate = meso- diaminoheptanedioate. Monomer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00300 Lysine biosynthesis

Compound table
Substrates Products Intermediates
KEGG-id C00666 C00680
E.C.
Compound LL-2,6-Diaminoheptanedioate meso-2,6-Diaminoheptanedioate
Type amino acids amino acids
ChEBI 16026
57609
16488
57791
PubChem 1549100
439283
1549101
99290
1bwzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1gqzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1bwzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1gqzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2], [8], [14]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bwzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 73
1gqzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 73
1bwzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 159;GLU 208;CYS 217
1gqzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 159;GLU 208;CYS 217

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.16457-16458
[3]
[8]
Fig.2, p.399-400
[13]
p.781-783
[14]
Fig.3, p.1706-1707

References
[1]
Resource
Comments
Medline ID
PubMed ID 6378903
Journal J Biol Chem
Year 1984
Volume 259
Pages 8907-14
Authors Wiseman JS, Nichols JS
Title Purification and properties of diaminopimelic acid epimerase from Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS)
Medline ID 99060082
PubMed ID 9843410
Journal Biochemistry
Year 1998
Volume 37
Pages 16452-8
Authors Cirilli M, Zheng R, Scapin G, Blanchard JS
Title Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.
Related PDB 1bwz
Related UniProtKB P44859
[3]
Resource
Comments
Medline ID
PubMed ID 10194362
Journal Biochemistry
Year 1999
Volume 38
Pages 4416-22
Authors Koo CW, Blanchard JS
Title Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10508663
Journal Curr Opin Chem Biol
Year 1999
Volume 3
Pages 607-13
Authors Born TL, Blanchard JS
Title Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10881998
Journal Bioorg Med Chem
Year 2000
Volume 8
Pages 843-71
Authors Cox RJ, Sutherland A, Vederas JC
Title Bacterial diaminopimelate metabolism as a target for antibiotic design.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 2000
Volume 122
Pages 6122-3
Authors Koo CW, Sutherland A, Vederas JC, Blanchard JS
Title Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12297289
Journal FEBS Lett
Year 2002
Volume 528
Pages 114-8
Authors Liu L, Iwata K, Yohda M, Miki K
Title Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 14747737
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 397-400
Authors Lloyd AJ, Huyton T, Turkenburg J, Roper DI
Title Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis.
Related PDB 1gqz
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 15449932
Journal Biochemistry
Year 2004
Volume 43
Pages 12427-35
Authors Parsons JF, Song F, Parsons L, Calabrese K, Eisenstein E, Ladner JE
Title Structure and function of the phenazine biosynthesis protein PhzF from Pseudomonas fluorescens 2-79.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 15545603
Journal Proc Natl Acad Sci U S A
Year 2004
Volume 101
Pages 16431-6
Authors Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV
Title Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 15103639
Journal Proteins
Year 2004
Volume 55
Pages 764-7
Authors Grassick A, Sulzenbacher G, Roig-Zamboni V, Campanacci V, Cambillau C, Bourne Y
Title Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 16327902
Journal Org Biomol Chem
Year 2005
Volume 3
Pages 4402-11
Authors Diaper CM, Sutherland A, Pillai B, James MN, Semchuk P, Blanchard JS, Vederas JC
Title The stereoselective synthesis of aziridine analogues of diaminopimelic acid (DAP) and their interaction with dap epimerase.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 16021630
Journal Proteins
Year 2005
Volume 60
Pages 778-86
Authors Liger D, Quevillon-Cheruel S, Sorel I, Bremang M, Blondeau K, Aboulfath I, Janin J, van Tilbeurgh H, Leulliot N
Title Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 16446443
Journal Proc Natl Acad Sci U S A
Year 2006
Volume 103
Pages 1705-10
Authors Buschiazzo A, Goytia M, Schaeffer F, Degrave W, Shepard W, Gregoire C, Chamond N, Cosson A, Berneman A, Coatnoan N, Alzari PM, Minoprio P
Title Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.
Related PDB
Related UniProtKB

Comments
This enzyme catalyzes racemization.

Created Updated
2004-04-05 2009-02-26