Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhizobium etli (strain CFN 42 / ATCC 51251)
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 sitei15SubstrateUniRule annotation1
Binding sitei47SubstrateUniRule annotation1
Binding sitei67SubstrateUniRule annotation1
Active sitei76Proton donorUniRule annotation1
Binding sitei163SubstrateUniRule annotation1
Sitei165Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Sitei215Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei224Proton 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:RHE_CH03955
OrganismiRhizobium etli (strain CFN 42 / ATCC 51251)
Taxonomic identifieri347834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupRhizobium
Proteomesi
  • UP000001936 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119441 – 301Diaminopimelate epimeraseAdd BLAST301

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi347834.RHE_CH03955.

Structurei

3D structure databases

ProteinModelPortaliQ2K386.
SMRiQ2K386.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni77 – 78Substrate bindingUniRule annotation2
Regioni215 – 216Substrate bindingUniRule annotation2
Regioni225 – 226Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMCGNGGR.

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.

Q2K386-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSATVEFARM NGLGNKILVV DMRGRSDKVT PAAAVALNAD PQTEFDQIMA
60 70 80 90 100
IHDPKADGTD AFIDILNSDG SKAQACGNGT RCVVQALAAE TGRKAFTFQT
110 120 130 140 150
VAGILNAIEH EDGTISVDMG KPVFDWDRIP LAEEFHDTSR IELQIGPIDN
160 170 180 190 200
PLLHSPSAMS MGNPHAIFWV DKDVMSYDLA RFGPLLENHP MFPERANITL
210 220 230 240 250
AQVTSPTTMT TRTWERGAGL TLACGSAACS AAVSAARTGR TGRKVKINVA
260 270 280 290 300
SAKPPAMLSI EWRERDDHVI MTGPAEWEWS GRLDPATGCW SRDDAREVEA

Q
Length:301
Mass (Da):32,593
Last modified:March 7, 2006 - v1
Checksum:i86441935EA898444
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000133 Genomic DNA. Translation: ABC92700.1.
RefSeqiWP_011427146.1. NC_007761.1.

Genome annotation databases

EnsemblBacteriaiABC92700; ABC92700; RHE_CH03955.
GeneIDi24301000.
KEGGiret:RHE_CH03955.

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.

Entry informationi

Entry nameiDAPF_RHIEC
AccessioniPrimary (citable) accession number: Q2K386
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: March 7, 2006
Last modified: June 7, 2017
This is version 71 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, Reference proteome

Documents

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