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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Thermobifida fusca (strain YX)
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 sitei11SubstrateUniRule annotation1
Binding sitei76SubstrateUniRule annotation1
Active sitei85Proton donorUniRule annotation1
Binding sitei157SubstrateUniRule annotation1
Sitei159Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei189SubstrateUniRule annotation1
Sitei207Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei216Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciTFUS269800:G1G4Q-831-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:Tfu_0816
OrganismiThermobifida fusca (strain YX)
Taxonomic identifieri269800 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptosporangialesNocardiopsaceaeThermobifida
Proteomesi
  • UP000000434 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992701 – 274Diaminopimelate epimeraseAdd BLAST274

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi269800.Tfu_0816

Structurei

3D structure databases

ProteinModelPortaliQ47RR3
SMRiQ47RR3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni86 – 87Substrate bindingUniRule annotation2
Regioni207 – 208Substrate bindingUniRule annotation2
Regioni217 – 218Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220467
KOiK01778
OMAiSMCGNGG
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.

Q47RR3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFAKGHGTE NDFVILPDPD GELDLDAATV AALCDRRAGL GADGVLRVVR
60 70 80 90 100
TKALDEPLTG EAATAQRCEW FMDYRNADGS VAEMCGNGVR VFARYLQEAG
110 120 130 140 150
LVGAAAFEVG TRAGARHVVL EPDGNITVDM GPVRILGPGS ARLADGPVHG
160 170 180 190 200
TRISVGNPHL ACRVARPVAE VDLSAPPLLR AEEFPQGANV EVFREVASGV
210 220 230 240 250
LEMRVYERGA AETRSCGTGI VAAAAAATPP GEDARWTVRV PGGECTVVLE
260 270
SGAARLSGPA VIVAEGDVRL SALR
Length:274
Mass (Da):28,547
Last modified:September 13, 2005 - v1
Checksum:i735D907C1084EECC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000088 Genomic DNA Translation: AAZ54854.1
RefSeqiWP_011291263.1, NC_007333.1

Genome annotation databases

EnsemblBacteriaiAAZ54854; AAZ54854; Tfu_0816
KEGGitfu:Tfu_0816

Similar proteinsi

Entry informationi

Entry nameiDAPF_THEFY
AccessioniPrimary (citable) accession number: Q47RR3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 13, 2005
Last modified: March 28, 2018
This is version 82 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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