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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Ruthia magnifica subsp. Calyptogena magnifica
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 sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donorUniRule annotation1
Binding sitei155SubstrateUniRule annotation1
Sitei157Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei188SubstrateUniRule annotation1
Sitei206Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei215Proton acceptorUniRule annotation1
Sitei265Important for dimerizationUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciCRUT413404:G1G7M-562-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:Rmag_0550
OrganismiRuthia magnifica subsp. Calyptogena magnifica
Taxonomic identifieri413404 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriasulfur-oxidizing symbiontsCandidatus Ruthia
Proteomesi
  • UP000002587 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119561 – 271Diaminopimelate epimeraseAdd BLAST271

Proteomic databases

PRIDEiA1AWJ5

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi413404.Rmag_0550

Structurei

3D structure databases

ProteinModelPortaliA1AWJ5
SMRiA1AWJ5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni206 – 207Substrate bindingUniRule annotation2
Regioni216 – 217Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG091H01QC

Family and domain databases

HAMAPiMF_00197 DAP_epimerase, 1 hit
InterProiView protein in InterPro
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit

Sequencei

Sequence statusi: Complete.

A1AWJ5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLINFVKMHG LGNDFMMVDN LAGDITFNAE QIANLANRHL GIGFDQLLLV
60 70 80 90 100
ETSNTKNVDF RYVIYNADGL EVEQCGNGAR CFAFFVSKKG LSNNNPIVVE
110 120 130 140 150
TRSGIINLYL NDDNTVRVDM GKPSFNPADI LLLVPQQSTY YQIEGFDLGA
160 170 180 190 200
VSIGNPHCVM LVEDVNTVDV SSIALRIQQS ELLPNQANIG FMQILNTHEI
210 220 230 240 250
NLRVYERGSG ETLACGSGAC AAVVYGVEQG LLKENVVAHL NGGDTLIEYI
260 270
QGGHVFLSGP VQFVFEGKVE I
Length:271
Mass (Da):29,578
Last modified:January 23, 2007 - v1
Checksum:iC2F605B4314CBAEE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000488 Genomic DNA Translation: ABL02302.1
RefSeqiWP_011737927.1, NC_008610.1

Genome annotation databases

EnsemblBacteriaiABL02302; ABL02302; Rmag_0550
KEGGirma:Rmag_0550

Similar proteinsi

Entry informationi

Entry nameiDAPF_RUTMC
AccessioniPrimary (citable) accession number: A1AWJ5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 70 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

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