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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Helicobacter pylori (strain P12)
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 sitei60SubstrateUniRule annotation1
Active sitei69Proton donorUniRule annotation1
Sitei152Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei181SubstrateUniRule annotation1
Sitei199Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei209Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciHPYL570508:G1GU0-608-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:HPP12_0572
OrganismiHelicobacter pylori (strain P12)
Taxonomic identifieri570508 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000008198 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992391 – 272Diaminopimelate epimeraseAdd BLAST272

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliB6JLE8
SMRiB6JLE8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni70 – 71Substrate bindingUniRule annotation2
Regioni199 – 200Substrate bindingUniRule annotation2
Regioni210 – 211Substrate 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.

B6JLE8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVFYKYSGSG NDFLITQSFK KKDFSNLAKQ VCHRHEGFGA DGLVIVLPSK
60 70 80 90 100
DYDYEWDFYN SDGSKAGMCG NASRCVGLFA YQHAIAPKEH VFLAGKREIS
110 120 130 140 150
ICIEEPNIIE SNLGNYKILD TIPNLRCKKF FTNNSVLENI LTFYLIDTGV
160 170 180 190 200
PHLVGFVKNK EWLNSLNTLE LRALRHAFNA NINIAFIENE ETIFLQTYER
210 220 230 240 250
GVEDFTLACG TGMAAVFIAA RLFYNAPKKA TLIPKSNESL ELSLKNDGIF
260 270
YKGIVRYIGM SVLGSVFENG CF
Length:272
Mass (Da):30,589
Last modified:December 16, 2008 - v1
Checksum:i2D6F88EA0AAFD36D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001217 Genomic DNA Translation: ACJ07726.1
RefSeqiWP_000232404.1, NC_011498.1

Genome annotation databases

EnsemblBacteriaiACJ07726; ACJ07726; HPP12_0572
KEGGihpp:HPP12_0572

Similar proteinsi

Entry informationi

Entry nameiDAPF_HELP2
AccessioniPrimary (citable) accession number: B6JLE8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: December 16, 2008
Last modified: March 28, 2018
This is version 55 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
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Main funding by: National Institutes of Health