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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Granulibacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei47 – 471SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei153 – 1531SubstrateUniRule annotation
Sitei155 – 1551Important for catalytic activityUniRule annotation
Binding sitei186 – 1861SubstrateUniRule annotation
Sitei204 – 2041Important for catalytic activityUniRule annotation
Active sitei213 – 2131Proton 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

BioCyciGBET391165:GHON-1537-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:GbCGDNIH1_1500
OrganismiGranulibacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1)
Taxonomic identifieri391165 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodospirillalesAcetobacteraceaeGranulibacter
ProteomesiUP000001963: Chromosome

Subcellular locationi

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 – 275275Diaminopimelate epimerasePRO_1000011883Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 213

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiQ0BS04.

Interactioni

Protein-protein interaction databases

STRINGi391165.GbCGDNIH1_1500.

Structurei

3D structure databases

ProteinModelPortaliQ0BS04.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni204 – 2052Substrate bindingUniRule annotation
Regioni214 – 2152Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
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.

Q0BS04-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLIDFIKMHG LGNDFVVFDA RKGPSLALSG SQAAAIADRR TGVGCDQLIV
60 70 80 90 100
LEPSTVADAF MRIYNPDGSE SGACGNATRC VADLLHRDGI AAPCMETVAG
110 120 130 140 150
LLLAEINGNG ICIDMGQPGL GWRDVPLARE MDTLFLPLEA PGLKMPAACS
160 170 180 190 200
MGNPHATFFV ADLAELDIPV TGPLLERHPL FPERANIGHA QMLSRSHIRL
210 220 230 240 250
RVWERGAGLT LACGTGACAT LVNAVRRGLA EREAVVELDG GQLLIHWREQ
260 270
DGHVLMTGPA ATVFHGRIAL ESITG
Length:275
Mass (Da):29,192
Last modified:October 17, 2006 - v1
Checksum:iC4C11D4AD427317A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000394 Genomic DNA. Translation: ABI62398.1.
RefSeqiWP_011632202.1. NC_008343.1.
YP_745321.1. NC_008343.1.

Genome annotation databases

EnsemblBacteriaiABI62398; ABI62398; GbCGDNIH1_1500.
GeneIDi4275809.
KEGGigbe:GbCGDNIH1_1500.
PATRICi22079183. VBIGraBet83793_1553.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000394 Genomic DNA. Translation: ABI62398.1.
RefSeqiWP_011632202.1. NC_008343.1.
YP_745321.1. NC_008343.1.

3D structure databases

ProteinModelPortaliQ0BS04.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi391165.GbCGDNIH1_1500.

Proteomic databases

PRIDEiQ0BS04.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABI62398; ABI62398; GbCGDNIH1_1500.
GeneIDi4275809.
KEGGigbe:GbCGDNIH1_1500.
PATRICi22079183. VBIGraBet83793_1553.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciGBET391165:GHON-1537-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. "Genome sequence analysis of the emerging human pathogenic acetic acid bacterium Granulibacter bethesdensis."
    Greenberg D.E., Porcella S.F., Zelazny A.M., Virtaneva K., Sturdevant D.E., Kupko J.J. III, Barbian K.D., Babar A., Dorward D.W., Holland S.M.
    J. Bacteriol. 189:8727-8736(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-1260 / CGDNIH1.

Entry informationi

Entry nameiDAPF_GRABC
AccessioniPrimary (citable) accession number: Q0BS04
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 17, 2006
Last modified: February 4, 2015
This is version 60 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.