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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Corynebacterium glutamicum (strain R)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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

Pathway:iL-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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei15 – 151SubstrateUniRule annotation
Binding sitei48 – 481SubstrateUniRule annotation
Binding sitei74 – 741SubstrateUniRule annotation
Active sitei83 – 831Proton donor/acceptorUniRule annotation
Binding sitei159 – 1591SubstrateUniRule annotation
Sitei161 – 1611Important for catalytic activityUniRule annotation
Binding sitei194 – 1941SubstrateUniRule annotation
Sitei212 – 2121Important for catalytic activityUniRule annotation
Active sitei221 – 2211Proton donor/acceptorUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciCGLU340322:GJBE-1853-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:cgR_1773
OrganismiCorynebacterium glutamicum (strain R)
Taxonomic identifieri340322 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
ProteomesiUP000006698 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 277277Diaminopimelate epimerasePRO_1000011872Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi83 ↔ 221

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliA4QEV1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni83 – 853Substrate bindingUniRule annotation
Regioni212 – 2132Substrate bindingUniRule annotation
Regioni222 – 2232Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMRIINSD.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A4QEV1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNLTIPFAKG HATENDFIII PDEDARLDLT PEMVVKLCDR RAGIGADGIL
60 70 80 90 100
RVVKAADVEG STVDPSLWFM DYRNADGSLA EMCGNGVRLF AHWLYSRSLV
110 120 130 140 150
DNTSFDIGTR AGVRHVDILQ ADQHSAQVRV DMGIPDVTGL STCDINGQVF
160 170 180 190 200
AGLGVDMGNP HLACVVPGLS ASALADMELR APTFDQEFFP HGVNVEIVTE
210 220 230 240 250
LEDDAVSMRV WERGVGETRS CGTGTVAAAC AALADAGLGE GTVKVCVPGG
260 270
EVEVQIFDDG STLTGPSAII ALGEVQI
Length:277
Mass (Da):29,260
Last modified:May 15, 2007 - v1
Checksum:iA540184C69079066
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009044 Genomic DNA. Translation: BAF54767.1.
RefSeqiWP_011897378.1. NC_009342.1.

Genome annotation databases

EnsemblBacteriaiBAF54767; BAF54767; cgR_1773.
KEGGicgt:cgR_1773.
PATRICi21508156. VBICorGlu58097_1825.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009044 Genomic DNA. Translation: BAF54767.1.
RefSeqiWP_011897378.1. NC_009342.1.

3D structure databases

ProteinModelPortaliA4QEV1.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF54767; BAF54767; cgR_1773.
KEGGicgt:cgR_1773.
PATRICi21508156. VBICorGlu58097_1825.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMRIINSD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCGLU340322:GJBE-1853-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R."
    Yukawa H., Omumasaba C.A., Nonaka H., Kos P., Okai N., Suzuki N., Suda M., Tsuge Y., Watanabe J., Ikeda Y., Vertes A.A., Inui M.
    Microbiology 153:1042-1058(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: R.

Entry informationi

Entry nameiDAPF_CORGB
AccessioniPrimary (citable) accession number: A4QEV1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 15, 2007
Last modified: July 22, 2015
This is version 55 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

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

External Data

Dasty 3

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 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.