Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
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 sitei17 – 171SubstrateUniRule annotation
Binding sitei49 – 491SubstrateUniRule annotation
Binding sitei69 – 691SubstrateUniRule annotation
Active sitei78 – 781Proton donor/acceptorUniRule annotation
Binding sitei166 – 1661SubstrateUniRule annotation
Sitei168 – 1681Important for catalytic activityUniRule annotation
Binding sitei199 – 1991SubstrateUniRule annotation
Sitei217 – 2171Important for catalytic activityUniRule annotation
Active sitei226 – 2261Proton 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

BioCyciOCAR504832:GJPZ-255-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:OCAR_4263, OCA5_c02550
OrganismiOligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
Taxonomic identifieri504832 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeOligotropha
ProteomesiUP000001678: Chromosome, UP000007730: 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 – 290290Diaminopimelate epimerasePRO_1000099253Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi78 ↔ 226

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi504832.OCAR_4263.

Structurei

3D structure databases

ProteinModelPortaliB6JAP3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 152Substrate bindingUniRule annotation
Regioni78 – 803Substrate bindingUniRule annotation
Regioni217 – 2182Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiILECFKV.
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.

B6JAP3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTVLANHSFA KMNGIGNEIV IVDLRNTDSQ LSAAEARAIA APGGVPYDQL
60 70 80 90 100
MVLQKPRMPG TTAFVRIYNN DGSEAGACGN GMRCVAKRVF GESGAQAATF
110 120 130 140 150
ETRAGLLNCW QGPSPDLYTV DMGTPKFGWQ DIPLAEEFRD TRYIELQIGP
160 170 180 190 200
IDAPVLHSPS VVSMGNPHAI FWVDDIEAYD LERLGPLLEN HPIFPERANI
210 220 230 240 250
TLAHVVDRNH IRMRTWERGA GLTLACGSAA CATAVAAARL KRTDRTVEMS
260 270 280 290
LPGGDLTIEW RESDDHVLMT GAAVLEYEGL FDPDLFAALA
Length:290
Mass (Da):31,496
Last modified:December 16, 2008 - v1
Checksum:i55349272902037E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001196 Genomic DNA. Translation: ACI91412.1.
CP002826 Genomic DNA. Translation: AEI04984.1.
RefSeqiWP_012561443.1. NC_015684.1.
YP_002287277.1. NC_011386.1.
YP_004631225.1. NC_015684.1.

Genome annotation databases

EnsemblBacteriaiACI91412; ACI91412; OCAR_4263.
AEI04984; AEI04984; OCA5_c02550.
GeneIDi10845387.
6993020.
KEGGioca:OCAR_4263.
ocg:OCA5_c02550.
PATRICi22802509. VBIOliCar134280_0245.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001196 Genomic DNA. Translation: ACI91412.1.
CP002826 Genomic DNA. Translation: AEI04984.1.
RefSeqiWP_012561443.1. NC_015684.1.
YP_002287277.1. NC_011386.1.
YP_004631225.1. NC_015684.1.

3D structure databases

ProteinModelPortaliB6JAP3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi504832.OCAR_4263.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACI91412; ACI91412; OCAR_4263.
AEI04984; AEI04984; OCA5_c02550.
GeneIDi10845387.
6993020.
KEGGioca:OCAR_4263.
ocg:OCA5_c02550.
PATRICi22802509. VBIOliCar134280_0245.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiILECFKV.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciOCAR504832:GJPZ-255-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 of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T."
    Paul D., Bridges S., Burgess S.C., Dandass Y., Lawrence M.L.
    J. Bacteriol. 190:5531-5532(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49405 / DSM 1227 / OM5.
  2. "Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5."
    Volland S., Rachinger M., Strittmatter A., Daniel R., Gottschalk G., Meyer O.
    J. Bacteriol. 193:5043-5043(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49405 / DSM 1227 / OM5.

Entry informationi

Entry nameiDAPF_OLICO
AccessioniPrimary (citable) accession number: B6JAP3
Secondary accession number(s): F8BTD9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: December 16, 2008
Last modified: January 7, 2015
This is version 42 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.