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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Burkholderia vietnamiensis (strain G4 / LMG 22486) (Burkholderia cepacia (strain R1808))
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 sitei67 – 671SubstrateUniRule annotation
Active sitei76 – 761Proton donor/acceptorUniRule annotation
Binding sitei167 – 1671SubstrateUniRule annotation
Sitei169 – 1691Important for catalytic activityUniRule annotation
Binding sitei200 – 2001SubstrateUniRule annotation
Sitei218 – 2181Important for catalytic activityUniRule annotation
Active sitei227 – 2271Proton 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

BioCyciBVIE269482:GJNA-3241-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:Bcep1808_3168
OrganismiBurkholderia vietnamiensis (strain G4 / LMG 22486) (Burkholderia cepacia (strain R1808))
Taxonomic identifieri269482 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex
ProteomesiUP000002287: Chromosome 1

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 – 289289Diaminopimelate epimerasePRO_1000011862Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 227

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi269482.Bcep1808_3168.

Structurei

3D structure databases

ProteinModelPortaliA4JIQ6.
SMRiA4JIQ6. Positions 3-287.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni76 – 783Substrate bindingUniRule annotation
Regioni218 – 2192Substrate bindingUniRule annotation
Regioni228 – 2292Substrate 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.

A4JIQ6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLSFTKMHG AGNDFVVLDG YSHTLPPLTD VQVRALADRH FGIGADQLLV
60 70 80 90 100
VEKPTVDGAD FKYRIFNCDG GEVEHCGNGA RCFVKFVTDR GLTDKRSVRV
110 120 130 140 150
QVMKGLITLT MQDNGEVVVD MGAPVFEPAQ VPFDASGLDG RTDGNDTLWP
160 170 180 190 200
LDVGGATRWV STVSMGNPHA VQVVDDAEAY PVLAEGPLIE RHARFPKRVN
210 220 230 240 250
AGFMQIVSRH EVKLRVYERG AGETLACGTG ACAAVAAGIR RGLLDTPVTV
260 270 280
HTHGGTLTIS WDGAHDERAA LTMAGPATTV FEGEIELNV
Length:289
Mass (Da):30,997
Last modified:May 1, 2007 - v1
Checksum:iD3EA718F216679FC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000614 Genomic DNA. Translation: ABO56159.1.
RefSeqiYP_001120994.1. NC_009256.1.

Genome annotation databases

EnsemblBacteriaiABO56159; ABO56159; Bcep1808_3168.
GeneIDi4954914.
KEGGibvi:Bcep1808_3168.
PATRICi19325026. VBIBurVie89221_7455.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000614 Genomic DNA. Translation: ABO56159.1.
RefSeqiYP_001120994.1. NC_009256.1.

3D structure databases

ProteinModelPortaliA4JIQ6.
SMRiA4JIQ6. Positions 3-287.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi269482.Bcep1808_3168.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABO56159; ABO56159; Bcep1808_3168.
GeneIDi4954914.
KEGGibvi:Bcep1808_3168.
PATRICi19325026. VBIBurVie89221_7455.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciBVIE269482:GJNA-3241-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. "Complete sequence of chromosome 1 of Burkholderia vietnamiensis G4."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.
    , Hauser L., Kyrpides N., Tiedje J., Richardson P.
    Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: G4 / LMG 22486.

Entry informationi

Entry nameiDAPF_BURVG
AccessioniPrimary (citable) accession number: A4JIQ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 1, 2007
Last modified: March 4, 2015
This is version 51 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.