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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111SubstrateUniRule annotation
Binding sitei42 – 421SubstrateUniRule annotation
Binding sitei60 – 601SubstrateUniRule annotation
Active sitei69 – 691Proton donor/acceptorUniRule annotation
Sitei152 – 1521Important for catalytic activityUniRule annotation
Binding sitei181 – 1811SubstrateUniRule annotation
Sitei199 – 1991Important for catalytic activityUniRule annotation
Active sitei209 – 2091Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciHPY:HP0566-MONOMER.
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:HP_0566
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
ProteomesiUP000000429 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 273273Diaminopimelate epimerasePRO_0000149843Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi69 ↔ 209

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiO25290.

Interactioni

Protein-protein interaction databases

IntActiO25290. 2 interactions.
STRINGi85962.HP0566.

Structurei

3D structure databases

ProteinModelPortaliO25290.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni69 – 713Substrate bindingUniRule annotation
Regioni199 – 2002Substrate bindingUniRule annotation
Regioni210 – 2112Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
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.

O25290-1 [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 VIPALRCEKF FSSGSVLEHI PTFYLIDTGV
160 170 180 190 200
PHLVGFVENK EGLNSLNTLE LRALRHEFNA NINIAFIENK ETIFLQTYER
210 220 230 240 250
GVEDFTLACG TGMAAVFIAA RIFYNTPKKA ALIPKSNESL ELSLKNDGIF
260 270
YKGAVRYIGM SVLGMRVFEN GCF
Length:273
Mass (Da):30,500
Last modified:January 1, 1998 - v1
Checksum:i73F3D7917AD35ACD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07622.1.
PIRiF64590.
RefSeqiNP_207361.1. NC_000915.1.
YP_006934488.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD07622; AAD07622; HP_0566.
GeneIDi899009.
KEGGiheo:C694_02920.
hpy:HP0566.
PATRICi20592405. VBIHelPyl33062_0591.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07622.1.
PIRiF64590.
RefSeqiNP_207361.1. NC_000915.1.
YP_006934488.1. NC_018939.1.

3D structure databases

ProteinModelPortaliO25290.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO25290. 2 interactions.
STRINGi85962.HP0566.

Proteomic databases

PRIDEiO25290.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07622; AAD07622; HP_0566.
GeneIDi899009.
KEGGiheo:C694_02920.
hpy:HP0566.
PATRICi20592405. VBIHelPyl33062_0591.

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciHPY:HP0566-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700392 / 26695.

Entry informationi

Entry nameiDAPF_HELPY
AccessioniPrimary (citable) accession number: O25290
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: April 29, 2015
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.