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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Helicobacter pylori (strain Shi470)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 sitei42SubstrateUniRule annotation1
Binding sitei60SubstrateUniRule annotation1
Active sitei69Proton donor/acceptorUniRule annotation1
Sitei152Important for catalytic activityUniRule annotation1
Binding sitei181SubstrateUniRule annotation1
Sitei199Important for catalytic activityUniRule annotation1
Active sitei209Proton donor/acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-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
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

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

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

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi69 ↔ 209

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliB2UTR2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni69 – 71Substrate bindingUniRule annotation3
Regioni199 – 200Substrate bindingUniRule annotation2
Regioni210 – 211Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiNTGSPHY.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

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.
PATRICi20612973. VBIHelPyl23559_0798.

Cross-referencesi

Sequence databases

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

3D structure databases

ProteinModelPortaliB2UTR2.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD48244; ACD48244; HPSH_04045.
KEGGihps:HPSH_04045.
PATRICi20612973. VBIHelPyl23559_0798.

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiNTGSPHY.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_HELPS
AccessioniPrimary (citable) accession number: B2UTR2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: November 2, 2016
This is version 56 of the entry and version 1 of the sequence. [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

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.