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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
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

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 sitei15SubstrateUniRule annotation1
Binding sitei47SubstrateUniRule annotation1
Binding sitei67SubstrateUniRule annotation1
Active sitei76Proton donor/acceptorUniRule annotation1
Binding sitei163SubstrateUniRule annotation1
Sitei165Important for catalytic activityUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Sitei215Important for catalytic activityUniRule annotation1
Active sitei224Proton donor/acceptorUniRule annotation1

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

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:Atu2695
ORF Names:AGR_C_4886
OrganismiAgrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
Taxonomic identifieri176299 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
Proteomesi
  • UP000000813 Componenti: Chromosome circular

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498151 – 299Diaminopimelate epimeraseAdd BLAST299

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi76 ↔ 224

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi176299.Atu2695.

Structurei

3D structure databases

ProteinModelPortaliQ8UC03.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni12 – 13Substrate bindingUniRule annotation2
Regioni76 – 78Substrate bindingUniRule annotation3
Regioni215 – 216Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiATLSIEW.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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.

Q8UC03-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADTVEFAKM NGLANKILVV DMRGRKDMVT PAAAIALNSN PATQFDQIMA
60 70 80 90 100
IHDPRVGGTD AFIDILNCDG TKAQACGNGT RCVVQALSSE TGKTSFTFQT
110 120 130 140 150
VAGILNAVEH EDGMISVDMG LPRFRWSDIP LSEEFHDTSR IELQIGPIDA
160 170 180 190 200
PILHSPAVMS MGNPHAIFWV DRDPMTFDLE RFGPLLENHP MFPEKANITL
210 220 230 240 250
AQVISDSALR TRTWERGAGL TLACGSAACA SAVSAARTGR TGRKVTIDVA
260 270 280 290
SSPVRVPLTI DWREDNHVVM TGPAEWEWSG SVDPVTGVWA RDAVERGAV
Length:299
Mass (Da):32,287
Last modified:June 1, 2002 - v1
Checksum:i08F560516ABA14BD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007869 Genomic DNA. Translation: AAK88415.1.
PIRiAF2907.
F97682.
RefSeqiNP_355630.1. NC_003062.2.
WP_010972495.1. NC_003062.2.

Genome annotation databases

EnsemblBacteriaiAAK88415; AAK88415; Atu2695.
GeneIDi1134733.
KEGGiatu:Atu2695.
PATRICi20815185. VBIAgrTum91616_2705.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007869 Genomic DNA. Translation: AAK88415.1.
PIRiAF2907.
F97682.
RefSeqiNP_355630.1. NC_003062.2.
WP_010972495.1. NC_003062.2.

3D structure databases

ProteinModelPortaliQ8UC03.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi176299.Atu2695.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK88415; AAK88415; Atu2695.
GeneIDi1134733.
KEGGiatu:Atu2695.
PATRICi20815185. VBIAgrTum91616_2705.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiATLSIEW.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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...

Entry informationi

Entry nameiDAPF_AGRFC
AccessioniPrimary (citable) accession number: Q8UC03
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 2002
Last sequence update: June 1, 2002
Last modified: September 7, 2016
This is version 84 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, 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.