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B8EM14

- DAPF_METSB

UniProt

B8EM14 - DAPF_METSB

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
Status
Reviewed - 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 sitei165 – 1651SubstrateUniRule annotation
Sitei167 – 1671Important for catalytic activityUniRule annotation
Binding sitei198 – 1981SubstrateUniRule annotation
Sitei216 – 2161Important for catalytic activityUniRule annotation
Active sitei225 – 2251Proton 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

BioCyciMSIL395965:GCND-1884-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:Msil_1850
OrganismiMethylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
Taxonomic identifieri395965 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMethylocella
ProteomesiUP000002257: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 290290Diaminopimelate epimerasePRO_1000124426Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi78 ↔ 225

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi395965.Msil_1850.

Structurei

3D structure databases

ProteinModelPortaliB8EM14.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 152Substrate bindingUniRule annotation
Regioni78 – 803Substrate bindingUniRule annotation
Regioni216 – 2172Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiDGVWMTG.
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.

B8EM14-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNPLANRLAV KMNGIGNEIL IVDLRGAGAG VTGPQARAIA RTKGLAFDQL
60 70 80 90 100
MVLEDPRSKG CAAFVTIFNA DGSQSAACGN GTRCVAWTLL KDGARDEVLL
110 120 130 140 150
ETAAGRLACR RVSELVFSVE MGRPRLKAAE IPLSRDAPDT SAVDLSFGPA
160 170 180 190 200
DSPILKNPAV VNMGNPHAIF FVEDIGAYDL AAIGPVLEHD PLFPERANIS
210 220 230 240 250
LARIVSPERI ELKVWERGVG LTLACGSAAC AALVAAARRG LTGRRATVAL
260 270 280 290
PGGELDIFWR ESDDMVVMTG PVAFEFETRL DPAIFADAAA
Length:290
Mass (Da):30,607
Last modified:March 3, 2009 - v1
Checksum:iCBA2F8F9AD691263
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001280 Genomic DNA. Translation: ACK50795.1.
RefSeqiYP_002362157.1. NC_011666.1.

Genome annotation databases

EnsemblBacteriaiACK50795; ACK50795; Msil_1850.
GeneIDi7094129.
KEGGimsl:Msil_1850.
PATRICi22599279. VBIMetSil55537_2008.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001280 Genomic DNA. Translation: ACK50795.1 .
RefSeqi YP_002362157.1. NC_011666.1.

3D structure databases

ProteinModelPortali B8EM14.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 395965.Msil_1850.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACK50795 ; ACK50795 ; Msil_1850 .
GeneIDi 7094129.
KEGGi msl:Msil_1850.
PATRICi 22599279. VBIMetSil55537_2008.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
KOi K01778.
OMAi DGVWMTG.
OrthoDBi EOG6ND0M5.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci MSIL395965:GCND-1884-MONOMER.

Family and domain databases

HAMAPi MF_00197. DAP_epimerase.
InterProi IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view ]
PANTHERi PTHR31689. PTHR31689. 1 hit.
Pfami PF01678. DAP_epimerase. 2 hits.
[Graphical view ]
TIGRFAMsi TIGR00652. DapF. 1 hit.
PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2."
    Chen Y., Crombie A., Rahman M.T., Dedysh S.N., Liesack W., Stott M.B., Alam M., Theisen A.R., Murrell J.C., Dunfield P.F.
    J. Bacteriol. 192:3840-3841(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: BL2 / DSM 15510 / NCIMB 13906.

Entry informationi

Entry nameiDAPF_METSB
AccessioniPrimary (citable) accession number: B8EM14
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: October 29, 2014
This is version 35 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