EzCatDB: D00454
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DB codeD00454
CATH domainDomain 13.10.310.10 : Diaminopimelate Epimerase; Chain A, domain 1Catalytic domain
Domain 23.10.310.10 : Diaminopimelate Epimerase; Chain A, domain 1Catalytic domain
E.C.5.1.1.7
CSA1bwz


Enzyme Name
UniProtKBKEGG

P44859
Protein nameDiaminopimelate epimerasediaminopimelate epimerase
SynonymsDAP epimerase
EC 5.1.1.7
RefSeqNP_438909.1 (Protein)
NC_000907.1 (DNA/RNA sequence)
PfamPF01678 (DAP_epimerase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00300Lysine biosynthesis

UniProtKB:Accession NumberP44859
Entry nameDAPF_HAEIN
ActivityLL-2,6-diaminoheptanedioate = meso- diaminoheptanedioate.
SubunitMonomer.
Subcellular locationCytoplasm.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00666C00680
CompoundLL-2,6-Diaminoheptanedioatemeso-2,6-Diaminoheptanedioate
Typeamino acidsamino acids
ChEBI16026
57609
16488
57791
PubChem439283
1549100
99290
1549101
          
1bwzA01UnboundUnbound
1gqzA01UnboundUnbound
1bwzA02UnboundUnbound
1gqzA02UnboundUnbound

Active-site residues
resource
literature [2], [8], [14]
pdbCatalytic residues
         
1bwzA01CYS  73
1gqzA01CYS  73
1bwzA02HIS 159;GLU 208;CYS 217
1gqzA02HIS 159;GLU 208;CYS 217

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID6378903
JournalJ Biol Chem
Year1984
Volume259
Pages8907-14
AuthorsWiseman JS, Nichols JS
TitlePurification and properties of diaminopimelic acid epimerase from Escherichia coli.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS)
Medline ID99060082
PubMed ID9843410
JournalBiochemistry
Year1998
Volume37
Pages16452-8
AuthorsCirilli M, Zheng R, Scapin G, Blanchard JS
TitleStructural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.
Related PDB1bwz
Related UniProtKBP44859
[3]
PubMed ID10194362
JournalBiochemistry
Year1999
Volume38
Pages4416-22
AuthorsKoo CW, Blanchard JS
TitleChemical mechanism of Haemophilus influenzae diaminopimelate epimerase.
[4]
PubMed ID10508663
JournalCurr Opin Chem Biol
Year1999
Volume3
Pages607-13
AuthorsBorn TL, Blanchard JS
TitleStructure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis.
[5]
PubMed ID10881998
JournalBioorg Med Chem
Year2000
Volume8
Pages843-71
AuthorsCox RJ, Sutherland A, Vederas JC
TitleBacterial diaminopimelate metabolism as a target for antibiotic design.
[6]
JournalJ Am Chem Soc
Year2000
Volume122
Pages6122-3
AuthorsKoo CW, Sutherland A, Vederas JC, Blanchard JS
TitleIdentification of active site cysteine residues that function as general bases: diaminopimelate epimerase.
[7]
PubMed ID12297289
JournalFEBS Lett
Year2002
Volume528
Pages114-8
AuthorsLiu L, Iwata K, Yohda M, Miki K
TitleStructural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases.
[8]
PubMed ID14747737
JournalActa Crystallogr D Biol Crystallogr
Year2004
Volume60
Pages397-400
AuthorsLloyd AJ, Huyton T, Turkenburg J, Roper DI
TitleRefinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis.
Related PDB1gqz
[9]
PubMed ID15449932
JournalBiochemistry
Year2004
Volume43
Pages12427-35
AuthorsParsons JF, Song F, Parsons L, Calabrese K, Eisenstein E, Ladner JE
TitleStructure and function of the phenazine biosynthesis protein PhzF from Pseudomonas fluorescens 2-79.
[10]
PubMed ID15545603
JournalProc Natl Acad Sci U S A
Year2004
Volume101
Pages16431-6
AuthorsBlankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV
TitleStructure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.
[11]
PubMed ID15103639
JournalProteins
Year2004
Volume55
Pages764-7
AuthorsGrassick A, Sulzenbacher G, Roig-Zamboni V, Campanacci V, Cambillau C, Bourne Y
TitleCrystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase.
[12]
PubMed ID16327902
JournalOrg Biomol Chem
Year2005
Volume3
Pages4402-11
AuthorsDiaper CM, Sutherland A, Pillai B, James MN, Semchuk P, Blanchard JS, Vederas JC
TitleThe stereoselective synthesis of aziridine analogues of diaminopimelic acid (DAP) and their interaction with dap epimerase.
[13]
PubMed ID16021630
JournalProteins
Year2005
Volume60
Pages778-86
AuthorsLiger D, Quevillon-Cheruel S, Sorel I, Bremang M, Blondeau K, Aboulfath I, Janin J, van Tilbeurgh H, Leulliot N
TitleCrystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
[14]
PubMed ID16446443
JournalProc Natl Acad Sci U S A
Year2006
Volume103
Pages1705-10
AuthorsBuschiazzo A, Goytia M, Schaeffer F, Degrave W, Shepard W, Gregoire C, Chamond N, Cosson A, Berneman A, Coatnoan N, Alzari PM, Minoprio P
TitleCrystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.

comments
This enzyme catalyzes racemization.

createdupdated
2004-04-052009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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