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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
Status
Reviewed-Annotation score: -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 sitei17SubstrateUniRule annotation1
Binding sitei47SubstrateUniRule annotation1
Binding sitei67SubstrateUniRule annotation1
Active sitei76Proton donorUniRule annotation1
Binding sitei164SubstrateUniRule annotation1
Sitei166Could 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

BioCyciRPAL258594:G1GT2-259-MONOMER
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:RPA0250
OrganismiRhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
Taxonomic identifieri258594 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeRhodopseudomonas
Proteomesi
  • UP000001426 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119481 – 293Diaminopimelate epimeraseAdd BLAST293

Proteomic databases

PRIDEiQ6ND59

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi258594.RPA0250

Structurei

3D structure databases

ProteinModelPortaliQ6ND59
SMRiQ6ND59
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
OMAiSMCGNGG
OrthoDBiPOG091H01QC
PhylomeDBiQ6ND59

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.

Q6ND59-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSALDNRLFA KMNGIGNEIV VVDLRDQPAP VTPADARAVA AHVPYDQLML
60 70 80 90 100
LQPARLSGTE AFVRIYNNDG SESGACGNGM RCVARQMFSG SEKNGLTFET
110 120 130 140 150
RAGLLNCWRG PADGLYTVDM GEPKFGWQDI PLAEEFRDTR MIELQIGPID
160 170 180 190 200
APVLHTPSVV SMGNPHAIFW VDDVNAYDLG RFGPLLENHP IFPERANITL
210 220 230 240 250
AHIVDRQHIT MRTWERGAGL TKACGSAACS TAVAAARLKR TDRTVEMTLP
260 270 280 290
GGQLTIEWRE SDNHVLMTGG AAFEFEGRFD PALFSGALDP TGA
Length:293
Mass (Da):31,885
Last modified:July 5, 2004 - v1
Checksum:i078D9364C9C7B56E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX572593 Genomic DNA Translation: CAE25694.1
RefSeqiWP_011155818.1, NC_005296.1

Genome annotation databases

EnsemblBacteriaiCAE25694; CAE25694; RPA0250
KEGGirpa:RPA0250

Similar proteinsi

Entry informationi

Entry nameiDAPF_RHOPA
AccessioniPrimary (citable) accession number: Q6ND59
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 5, 2004
Last modified: May 23, 2018
This is version 81 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
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