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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Bartonella quintana (strain Toulouse) (Rochalimaea quintana)
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 sitei13SubstrateUniRule annotation1
Binding sitei45SubstrateUniRule annotation1
Binding sitei65SubstrateUniRule annotation1
Active sitei74Proton donorUniRule annotation1
Binding sitei156SubstrateUniRule annotation1
Sitei158Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei190SubstrateUniRule annotation1
Sitei208Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei217Proton 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:BQ13480
OrganismiBartonella quintana (strain Toulouse) (Rochalimaea quintana)
Taxonomic identifieri283165 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBartonellaceaeBartonella
Proteomesi
  • UP000000597 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000118471 – 283Diaminopimelate epimeraseAdd BLAST283

Proteomic databases

PRIDEiQ6FYC7.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi283165.BQ13480.

Structurei

3D structure databases

ProteinModelPortaliQ6FYC7.
SMRiQ6FYC7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni75 – 76Substrate bindingUniRule annotation2
Regioni208 – 209Substrate bindingUniRule annotation2
Regioni218 – 219Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiNGMRCVV.
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.

Q6FYC7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTPFRKMDG LGNQIIVADM RESTHALTPQ AILALAADPQ THFDQIMTIH
60 70 80 90 100
SSTQKEADFR IEIWNADGSM AKACGNGTRC VIAWLTDHNL GESFRLETPA
110 120 130 140 150
GIIEGKRQTD NLISVDMGCP NFNAKEMPVS REIADTNYVK ITAGPLKDAC
160 170 180 190 200
LVSIGNLHAI FFVEDNIQQI PLEKYGPKLE HDPLFPERCN ISIASVTSHK
210 220 230 240 250
SLNLRTWERG AGLTKACGSA ACASAVAAYR RGLTQRHIDV NLPGGTLNIV
260 270 280
YREDNHIVMT GPTKYEFGGF LNPLTGTYKK DHF
Length:283
Mass (Da):31,158
Last modified:July 19, 2004 - v1
Checksum:i14EFF366FAAA94C9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX897700 Genomic DNA. Translation: CAF26806.1.
RefSeqiWP_011179960.1. NC_005955.1.

Genome annotation databases

EnsemblBacteriaiCAF26806; CAF26806; BQ13480.
KEGGibqu:BQ13480.
PATRICi31954173. VBIBarQui58630_1483.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX897700 Genomic DNA. Translation: CAF26806.1.
RefSeqiWP_011179960.1. NC_005955.1.

3D structure databases

ProteinModelPortaliQ6FYC7.
SMRiQ6FYC7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi283165.BQ13480.

Proteomic databases

PRIDEiQ6FYC7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAF26806; CAF26806; BQ13480.
KEGGibqu:BQ13480.
PATRICi31954173. VBIBarQui58630_1483.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiNGMRCVV.
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_BARQU
AccessioniPrimary (citable) accession number: Q6FYC7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 19, 2004
Last modified: March 15, 2017
This is version 76 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

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.