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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhizobium leguminosarum bv. trifolii (strain WSM2304)
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:Rleg2_3748
OrganismiRhizobium leguminosarum bv. trifolii (strain WSM2304)
Taxonomic identifieri395492 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupRhizobium
Proteomesi
  • UP000008330 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992591 – 301Diaminopimelate epimeraseAdd BLAST301

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi395492.Rleg2_3748.

Structurei

3D structure databases

ProteinModelPortaliB5ZTH4.
SMRiB5ZTH4.
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.

B5ZTH4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSATVEFARM NGLGNKILVV DMRGRPDKVT PAAAVALNAD PQTEFDQIMA
60 70 80 90 100
IHDPKADGTD AFIDILNSDG SKAQACGNGT RCVVQALAAE TGRKAFTFQT
110 120 130 140 150
VAGILNAVEH EDGTISVDMG RPVFDWNRIP LAEEFHDTSR IELQIGPIDN
160 170 180 190 200
PVLHSPSAMS MGNPHAIFWV DRDVMSYDLA RFGPLLENHP MFPERANITL
210 220 230 240 250
AQVTSPTSMT TRTWERGAGL TLACGSAACS AAVSAARTGR TGRKVTINVA
260 270 280 290 300
SAKPPATLSI EWRERDDHVI MTGPAEWEWS GSLDPSTGLW SRDGTQEAGA

R
Length:301
Mass (Da):32,387
Last modified:November 25, 2008 - v1
Checksum:iB915EA356E415DF5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001191 Genomic DNA. Translation: ACI57010.1.
RefSeqiWP_012559263.1. NC_011369.1.

Genome annotation databases

EnsemblBacteriaiACI57010; ACI57010; Rleg2_3748.
GeneIDi34191382.
KEGGirlt:Rleg2_3748.

Similar proteinsi

Entry informationi

Entry nameiDAPF_RHILW
AccessioniPrimary (citable) accession number: B5ZTH4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: November 25, 2008
Last modified: November 22, 2017
This is version 54 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