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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rickettsia massiliae (strain Mtu5)
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 sitei15SubstrateUniRule annotation1
Binding sitei49SubstrateUniRule 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 sitei187SubstrateUniRule annotation1
Sitei204Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei213Proton 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:RMA_0596
OrganismiRickettsia massiliae (strain Mtu5)
Taxonomic identifieri416276 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiaspotted fever group
Proteomesi
  • UP000001311 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000585441 – 270Diaminopimelate epimeraseAdd BLAST270

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliA8F1I9
SMRiA8F1I9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni204 – 205Substrate bindingUniRule annotation2
Regioni214 – 215Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG

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.

A8F1I9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MISKINFVKM HGLGNDFVIV NKRDLSSSYD LSQLAKNMAE RHTGIGCDQF
60 70 80 90 100
IIYEEHNDFY EMIIYNIDGS SAKLCGNATR CLAKLIYLDT GKKDITVMVG
110 120 130 140 150
NKKLLCNVND ENNISVNVGS VSFNEAWMPS RDKVWAFAER YMIDLKETIC
160 170 180 190 200
VDIGNPHLII FSKLEPQDQK IVGEKLQAKE LFADGVNVNF AEVKDNKIYL
210 220 230 240 250
SVWERGAGLT LACGSGACGS FAAGLKLGFI HSPSTIVFKH GNLTMKEENG
260 270
NIIMQGAATL VARGEYYCEQ
Length:270
Mass (Da):29,957
Last modified:November 13, 2007 - v1
Checksum:i643AA4CF2B84CB12
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000683 Genomic DNA Translation: ABV84775.1
RefSeqiWP_012152750.1, NC_009900.1

Genome annotation databases

EnsemblBacteriaiABV84775; ABV84775; RMA_0596
KEGGirms:RMA_0596

Similar proteinsi

Entry informationi

Entry nameiDAPF_RICM5
AccessioniPrimary (citable) accession number: A8F1I9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: November 13, 2007
Last modified: March 28, 2018
This is version 59 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