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A2SKV9

- DAPF_METPP

UniProt

A2SKV9 - DAPF_METPP

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylibium petroleiphilum (strain PM1)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei46 – 461SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei75 – 751Proton donor/acceptorUniRule annotation
Binding sitei166 – 1661SubstrateUniRule annotation
Sitei168 – 1681Important for catalytic activityUniRule annotation
Binding sitei204 – 2041SubstrateUniRule annotation
Sitei222 – 2221Important for catalytic activityUniRule annotation
Active sitei231 – 2311Proton 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

BioCyciMPET420662:GHBE-3283-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:Mpe_A3245
OrganismiMethylibium petroleiphilum (strain PM1)
Taxonomic identifieri420662 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesMethylibium
ProteomesiUP000000366: 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 – 296296Diaminopimelate epimerasePRO_1000011904Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 231

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi420662.Mpe_A3245.

Structurei

3D structure databases

ProteinModelPortaliA2SKV9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 773Substrate bindingUniRule annotation
Regioni222 – 2232Substrate bindingUniRule annotation
Regioni232 – 2332Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLIVEPPY.
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.

A2SKV9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKLRFTKMQG AGNDFVVLDA TREPLTLSPA QYRYLADRRF GVGADQVLIV
60 70 80 90 100
GASDEPGIDF TYRIVNADGS EVEQCGNGAR CFVRYVREAG LTKKSAIRVR
110 120 130 140 150
TAGGVIEPRW LVDGRVTVDM GAPVFEPARV PFDAAGLQPR ELNGFALWPL
160 170 180 190 200
DAADRTVEAA VVSMGNPHAV MNVAQFGSGG VDEAPVAELG PLVERHTRFP
210 220 230 240 250
QRVNAGFLQV LSDTHVKLRV YERGAGETLA CGTGACAAVV AGIRLGWLRA
260 270 280 290
GTPVDVDTRG GELTIEWAGR SDAPVWMTGP AESVYVGEID LPEQGD
Length:296
Mass (Da):31,697
Last modified:March 6, 2007 - v1
Checksum:i7AB9E380A6C0A088
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000555 Genomic DNA. Translation: ABM96198.1.
RefSeqiYP_001022433.1. NC_008825.1.

Genome annotation databases

EnsemblBacteriaiABM96198; ABM96198; Mpe_A3245.
GeneIDi4786524.
KEGGimpt:Mpe_A3245.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000555 Genomic DNA. Translation: ABM96198.1 .
RefSeqi YP_001022433.1. NC_008825.1.

3D structure databases

ProteinModelPortali A2SKV9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 420662.Mpe_A3245.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABM96198 ; ABM96198 ; Mpe_A3245 .
GeneIDi 4786524.
KEGGi mpt:Mpe_A3245.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci MPET420662:GHBE-3283-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. "Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1."
    Kane S.R., Chakicherla A.Y., Chain P.S.G., Schmidt R., Shin M.W., Legler T.C., Scow K.M., Larimer F.W., Lucas S.M., Richardson P.M., Hristova K.R.
    J. Bacteriol. 189:1931-1945(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PM1.

Entry informationi

Entry nameiDAPF_METPP
AccessioniPrimary (citable) accession number: A2SKV9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: March 6, 2007
Last modified: October 29, 2014
This is version 55 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