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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Bartonella tribocorum (strain CIP 105476 / IBS 506)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei45 – 451SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei156 – 1561SubstrateUniRule annotation
Sitei158 – 1581Important for catalytic activityUniRule annotation
Binding sitei190 – 1901SubstrateUniRule annotation
Sitei208 – 2081Important for catalytic activityUniRule annotation
Active sitei217 – 2171Proton 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

BioCyciBTRI382640:GJEK-2136-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:BT_2682
OrganismiBartonella tribocorum (strain CIP 105476 / IBS 506)
Taxonomic identifieri382640 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBartonellaceaeBartonella
ProteomesiUP000001592 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 – 283283Diaminopimelate epimerasePRO_1000077690Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 217

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi382640.Btr_2682.

Structurei

3D structure databases

ProteinModelPortaliA9IZW1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni208 – 2092Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000290798.
KOiK01778.
OMAiISIMNIL.
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.

A9IZW1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTPFSKMDG LGNQIIVADM RESTQALTPQ AILALSADPE MHFDQIMAIR
60 70 80 90 100
NPTKNEADFH IEIWNADGSK AKACGNGTRC VIAWLTDHNF GENFRLEAPT
110 120 130 140 150
GIIEGKRQAD NLISVDMGCP NFNAKEMPVS REIVDTNHID ITAGPLKDAC
160 170 180 190 200
LISIGNLHAI FFVENDVQHI PLEKYGPKLE HDPLFPERCN ISIACITSKK
210 220 230 240 250
SLNLRTWERG AGLTQACGSA ACAGAVAAYR RSLTQRHIDV NLPGGKLNIF
260 270 280
YREDDHIIMT GPIKYQFSGF LNPLTGCYKK DNS
Length:283
Mass (Da):31,231
Last modified:February 5, 2008 - v1
Checksum:i08A7EE32CC7E108B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM260525 Genomic DNA. Translation: CAK02629.1.
RefSeqiWP_012232622.1. NC_010161.1.

Genome annotation databases

KEGGibtr:Btr_2682.
PATRICi20553228. VBIBarTri113218_2730.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM260525 Genomic DNA. Translation: CAK02629.1.
RefSeqiWP_012232622.1. NC_010161.1.

3D structure databases

ProteinModelPortaliA9IZW1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi382640.Btr_2682.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGibtr:Btr_2682.
PATRICi20553228. VBIBarTri113218_2730.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000290798.
KOiK01778.
OMAiISIMNIL.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciBTRI382640:GJEK-2136-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. "Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors."
    Saenz H.L., Engel P., Stoeckli M.C., Lanz C., Raddatz G., Vayssier-Taussat M., Birtles R., Schuster S.C., Dehio C.
    Nat. Genet. 39:1469-1476(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CIP 105476 / IBS 506.

Entry informationi

Entry nameiDAPF_BART1
AccessioniPrimary (citable) accession number: A9IZW1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: February 5, 2008
Last modified: July 22, 2015
This is version 54 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.