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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Pseudomonas stutzeri (strain A1501)
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 sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donorUniRule annotation1
Binding sitei159SubstrateUniRule annotation1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei192SubstrateUniRule annotation1
Sitei210Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei219Proton acceptorUniRule annotation1
Sitei270Important for dimerizationUniRule 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:PST_0510
OrganismiPseudomonas stutzeri (strain A1501)
Taxonomic identifieri379731 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000000233 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119371 – 276Diaminopimelate epimeraseAdd BLAST276

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi379731.PST_0510.

Structurei

3D structure databases

ProteinModelPortaliA4VGW5.
SMRiA4VGW5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni210 – 211Substrate bindingUniRule annotation2
Regioni220 – 221Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMCGNGGR.
OrthoDBiPOG091H01QC.

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.

A4VGW5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLRFTKMHG LGNDFMVIDL VSQHAHIQPK HAKQWGDRHT GVGFDQLLIV
60 70 80 90 100
EPPQNPDVDF RYRIFNSDGS EVEQCGNGAR CFARFVVDKR LTVKRKIKVE
110 120 130 140 150
TKGGIIELDI RPDGQIRVDM GPPRLVPAEI PFQAEREALS YSLEVDGQQV
160 170 180 190 200
ELAAASMGNP HAVLRVDSVE RAPVHELGPK IEHHPRFPQR VNVGFLQVVD
210 220 230 240 250
RRHARLRVWE RGAGETQACG TGACAAAVAA IRQGWMDSPV QIELPGGRLS
260 270
IEWAGPGQPV MMTGPAVRVF EGQVRL
Length:276
Mass (Da):30,634
Last modified:May 29, 2007 - v1
Checksum:i1767C5F352337890
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000304 Genomic DNA. Translation: ABP78216.1.
RefSeqiWP_011911743.1. NC_009434.1.

Genome annotation databases

EnsemblBacteriaiABP78216; ABP78216; PST_0510.
KEGGipsa:PST_0510.

Similar proteinsi

Entry informationi

Entry nameiDAPF_PSEU5
AccessioniPrimary (citable) accession number: A4VGW5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 29, 2007
Last modified: September 27, 2017
This is version 67 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