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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Vesicomyosocius okutanii subsp. Calyptogena okutanii (strain HA)
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 sitei46 – 461SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei75 – 751Proton donor/acceptorUniRule annotation
Binding sitei155 – 1551SubstrateUniRule annotation
Sitei157 – 1571Important for catalytic activityUniRule annotation
Binding sitei188 – 1881SubstrateUniRule annotation
Sitei206 – 2061Important for catalytic activityUniRule annotation
Active sitei215 – 2151Proton 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

BioCyciCVES412965:GHZZ-504-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:COSY_0505
OrganismiVesicomyosocius okutanii subsp. Calyptogena okutanii (strain HA)
Taxonomic identifieri412965 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriasulfur-oxidizing symbionts
ProteomesiUP000000247 Componenti: 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 – 271271Diaminopimelate epimerasePRO_1000011980Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 215

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi412965.COSY_0505.

Structurei

3D structure databases

ProteinModelPortaliA5CWN5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni75 – 773Substrate bindingUniRule annotation
Regioni206 – 2072Substrate 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.

A5CWN5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLINFTKMHG LGNDFMVVDN LAGDITFNAK KITNLANRAF GIGFDQLLVV
60 70 80 90 100
ETSNIRGVDF RYVIYNSNGS EVEQCGNGAR CFARFVNYKN LTHSNPITVK
110 120 130 140 150
TRSNIISLHL NDDNTVCVDM GKPSFNPADI PLLVPQQSEY YQIEGFDLGA
160 170 180 190 200
ISIGNPHCVM LVKDVNTIDV NTIALKIQQS ELLPNQANIG FMQILNTHEI
210 220 230 240 250
NLRVYERGSE ETLACGSGAC AAVAYGVEQG LLKKNVVVHL SGGDALIEYT
260 270
QGGHIFLSGP AQFVFEGQVE I
Length:271
Mass (Da):29,633
Last modified:June 12, 2007 - v1
Checksum:i0A9DC34BE57122A3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009247 Genomic DNA. Translation: BAF61624.1.
RefSeqiWP_011929894.1. NC_009465.1.
YP_001219348.1. NC_009465.1.

Genome annotation databases

EnsemblBacteriaiBAF61624; BAF61624; COSY_0505.
KEGGivok:COSY_0505.
PATRICi32020847. VBICanVes128383_0503.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009247 Genomic DNA. Translation: BAF61624.1.
RefSeqiWP_011929894.1. NC_009465.1.
YP_001219348.1. NC_009465.1.

3D structure databases

ProteinModelPortaliA5CWN5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi412965.COSY_0505.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF61624; BAF61624; COSY_0505.
KEGGivok:COSY_0505.
PATRICi32020847. VBICanVes128383_0503.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCVES412965:GHZZ-504-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. "Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii."
    Kuwahara H., Yoshida T., Takaki Y., Shimamura S., Nishi S., Harada M., Matsuyama K., Takishita K., Kawato M., Uematsu K., Fujiwara Y., Sato T., Kato C., Kitagawa M., Kato I., Maruyama T.
    Curr. Biol. 17:881-886(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HA.

Entry informationi

Entry nameiDAPF_VESOH
AccessioniPrimary (citable) accession number: A5CWN5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 12, 2007
Last modified: April 1, 2015
This is version 53 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

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.