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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
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

Pathway:iL-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

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

GO - Biological processi

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 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

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.
OMAiGMGNPHC.
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:
EMBLi
GenBanki
DDBJi
Links Updated
CP001280 Genomic DNA. Translation: ACK50795.1.
RefSeqiWP_012590865.1. NC_011666.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001280 Genomic DNA. Translation: ACK50795.1.
RefSeqiWP_012590865.1. NC_011666.1.

3D structure databases

ProteinModelPortaliB8EM14.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi395965.Msil_1850.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiGMGNPHC.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMSIL395965:GCND-1884-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 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: July 22, 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.