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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Helicobacter pylori (strain Shi470)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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

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:HPSH_04045
OrganismiHelicobacter pylori (strain Shi470)
Taxonomic identifieri512562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992411 – 273Diaminopimelate epimeraseAdd BLAST273

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliB2UTR2.
SMRiB2UTR2.
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.
OMAiMCGNGGR.

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.

B2UTR2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVFYKYSGSG NDFLIVQSFK KKDFSNLAKQ VCHRHEGFGA DGLVVVLPSK
60 70 80 90 100
DYDYEWDFYN SDGSKAGMCG NASRCVGLFA YQHAIASKNH VFLAGKREIS
110 120 130 140 150
ICIEEPNIIE SNLGNYKILD TIPALRCEKF FTNDSVLENI PTFYLIDTGV
160 170 180 190 200
PHLVGFVKNK EWLNSLNTLE LRALRHAFNA NINIAFIENK ETIFLQTYER
210 220 230 240 250
GVEDFTLACG TGMAAVFIAA RIFYNTPEKA ALIPKSSESL ELSLKNDEIF
260 270
YKGAVRYIGM SVLGMSVFEN GCF
Length:273
Mass (Da):30,625
Last modified:July 1, 2008 - v1
Checksum:iB8F431A3C98A6A3E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001072 Genomic DNA. Translation: ACD48244.1.
RefSeqiWP_000232457.1. NC_010698.2.

Genome annotation databases

EnsemblBacteriaiACD48244; ACD48244; HPSH_04045.
KEGGihps:HPSH_04045.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiDAPF_HELPS
AccessioniPrimary (citable) accession number: B2UTR2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: June 7, 2017
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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families