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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rickettsia bellii (strain RML369-C)
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 sitei49SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donor/acceptorUniRule annotation1
Binding sitei155SubstrateUniRule annotation1
Sitei157Important for catalytic activityUniRule annotation1
Binding sitei187SubstrateUniRule annotation1
Sitei204Important for catalytic activityUniRule annotation1
Active sitei213Proton 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:RBE_0652
OrganismiRickettsia bellii (strain RML369-C)
Taxonomic identifieri336407 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiabelli group
Proteomesi
  • UP000001951 Componenti: Chromosome

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_00002780441 – 269Diaminopimelate epimeraseAdd BLAST269

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi75 ↔ 213

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliQ1RIT1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni12 – 13Substrate bindingUniRule annotation2
Regioni75 – 77Substrate bindingUniRule annotation3
Regioni204 – 205Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiFILDQTE.
OrthoDBiPOG091H01QC.

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.

Q1RIT1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSKINFVKM HGLGNDFVII NKKDLTGTYD LSQLAKSMAK RHLGIGCDQF
60 70 80 90 100
IIYEEQNDSY EMIIYNIDGS SAKLCGNATR CLAKLIYLDT GKKDITVVVG
110 120 130 140 150
NKKLLCHVID ENNISVNVGG VSFNESWMPS RDKIWEFAER YMIDLKETIC
160 170 180 190 200
VDVGNPHLVI FSKLELQDQK IVGEKLQDKA LFADGVNVNF AEVRDNKIYL
210 220 230 240 250
SVWERGSGLT LACGSGACGS FAAGLKLGFI HSPCEVVFKH GSLIMKEENG
260
NIIMQGPASL VAKGMYYCE
Length:269
Mass (Da):29,769
Last modified:May 16, 2006 - v1
Checksum:i0F6C382EA4F5B6D3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000087 Genomic DNA. Translation: ABE04733.1.
RefSeqiWP_011477321.1. NC_007940.1.

Genome annotation databases

EnsemblBacteriaiABE04733; ABE04733; RBE_0652.
KEGGirbe:RBE_0652.
PATRICi17882762. VBIRicBel102610_0748.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000087 Genomic DNA. Translation: ABE04733.1.
RefSeqiWP_011477321.1. NC_007940.1.

3D structure databases

ProteinModelPortaliQ1RIT1.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABE04733; ABE04733; RBE_0652.
KEGGirbe:RBE_0652.
PATRICi17882762. VBIRicBel102610_0748.

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiFILDQTE.
OrthoDBiPOG091H01QC.

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_RICBR
AccessioniPrimary (citable) accession number: Q1RIT1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 20, 2007
Last sequence update: May 16, 2006
Last modified: November 2, 2016
This is version 67 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. Rickettsia bellii strain RML369-C
    Rickettsia bellii (strain RML369-C): entries and gene names
  3. 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.