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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Corynebacterium aurimucosum (strain ATCC 700975 / DSM 44827 / CN-1) (Corynebacterium nigricans)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei11SubstrateUniRule annotation1
Binding sitei75SubstrateUniRule annotation1
Active sitei84Proton donorUniRule annotation1
Binding sitei160SubstrateUniRule annotation1
Sitei162Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei195SubstrateUniRule annotation1
Sitei213Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei222Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Alternative name(s):
PLP-independent amino acid racemaseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:cauri_1487
OrganismiCorynebacterium aurimucosum (strain ATCC 700975 / DSM 44827 / CN-1) (Corynebacterium nigricans)
Taxonomic identifieri548476 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000002077 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001244081 – 278Diaminopimelate epimeraseAdd BLAST278

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi548476.CaurA7_010100009918.

Structurei

3D structure databases

ProteinModelPortaliC3PGX6.
SMRiC3PGX6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni85 – 86Substrate bindingUniRule annotation2
Regioni213 – 214Substrate bindingUniRule annotation2
Regioni223 – 224Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMCGNGGR.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiView protein in PROSITE
PS01326. DAP_EPIMERASE. 1 hit.

Sequencei

Sequence statusi: Complete.

C3PGX6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFAKGHGTE NDFVIVEGTG PLPPEKVVAL CDRRAGIGAD GVLRIIRAGE
60 70 80 90 100
LLASGEIDEL APGINADDWF MDYRNADGSV AEMCGNGTRV FAHWVRSRGL
110 120 130 140 150
LEEDTFTVGT RAGAKQVTVH SFSETEAEVS VEMGPAQVLG VSTASMAGES
160 170 180 190 200
FAGLGVDMGN PHLAAVIPGL TAEDLAAKRL EQPVFDADFF PAGVNVELVT
210 220 230 240 250
PLCDGVIHMR VFERGSGETR SCGTGTVAAA CAALADASQV TGHVRVIVPG
260 270
GEVEVEITED GSTLTGPSRI VATGETSL
Length:278
Mass (Da):28,854
Last modified:June 16, 2009 - v1
Checksum:i440E5C816AF40113
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001601 Genomic DNA. Translation: ACP33080.1.
RefSeqiWP_010190270.1. NZ_ACLH01000083.1.

Genome annotation databases

EnsemblBacteriaiACP33080; ACP33080; cauri_1487.
KEGGicar:cauri_1487.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001601 Genomic DNA. Translation: ACP33080.1.
RefSeqiWP_010190270.1. NZ_ACLH01000083.1.

3D structure databases

ProteinModelPortaliC3PGX6.
SMRiC3PGX6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi548476.CaurA7_010100009918.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACP33080; ACP33080; cauri_1487.
KEGGicar:cauri_1487.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMCGNGGR.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiView protein in PROSITE
PS01326. DAP_EPIMERASE. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_CORA7
AccessioniPrimary (citable) accession number: C3PGX6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: June 16, 2009
Last modified: June 7, 2017
This is version 49 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.