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B7VMD4

- DAPF_VIBSL

UniProt

B7VMD4 - DAPF_VIBSL

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Protein
Diaminopimelate epimerase
Gene
dapF, VS_3047
Organism
Vibrio splendidus (strain LGP32) (Vibrio splendidus (strain Mel32))
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 By similarity.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei13 – 131Substrate By similarity
Binding sitei46 – 461Substrate By similarity
Binding sitei66 – 661Substrate By similarity
Active sitei75 – 751Proton donor/acceptor By similarity
Binding sitei159 – 1591Substrate By similarity
Sitei161 – 1611Important for catalytic activity By similarity
Binding sitei192 – 1921Substrate By similarity
Sitei210 – 2101Important for catalytic activity By similarity
Active sitei219 – 2191Proton donor/acceptor By similarity

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP
Complete GO annotation...

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

BioCyciVSPL575788:GH64-2985-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase (EC:5.1.1.7)
Short name:
DAP epimerase
Gene namesi
Name:dapF
Ordered Locus Names:VS_3047
OrganismiVibrio splendidus (strain LGP32) (Vibrio splendidus (strain Mel32))
Taxonomic identifieri575788 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000009100: Chromosome 1

Subcellular locationi

Cytoplasm By similarity 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 – 276276Diaminopimelate epimeraseUniRule annotation
PRO_1000124433Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 219UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi575788.VS_3047.

Structurei

3D structure databases

ProteinModelPortaliB7VMD4.
SMRiB7VMD4. Positions 4-272.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate binding By similarity
Regioni75 – 773Substrate binding By similarity
Regioni210 – 2112Substrate binding By similarity

Sequence similaritiesi

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.

B7VMD4-1 [UniParc]FASTAAdd to Basket

« Hide

MHFHFSKMHG LGNDFMVVDC ITQNIFFSPD LIRRLADRHT GVGFDQLLVV    50
EAPYDPETDF HYRIFNADGS EVEQCGNGAR CFARFVRMKG LTNKYSINVS 100
TKKGKMVLKI EDNDLITVNM GIPEFEPGKI PFKAKQPEKT YILRTDVHTL 150
FCGAVSMGNP HVVTVVDDVD TADVDTLGPL LESHERFPER VNAGFMQVVN 200
REEVRLRVYE RGAGETQACG SGACGAVAVG ITQGLLAENV KVRLPGGDLH 250
ISWQGPGKPL LMTGPATHVF DGQLSC 276
Length:276
Mass (Da):30,411
Last modified:February 10, 2009 - v1
Checksum:iB0989A43779F0529
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
FM954972 Genomic DNA. Translation: CAV20325.1.
RefSeqiYP_002418565.1. NC_011753.2.

Genome annotation databases

EnsemblBacteriaiCAV20325; CAV20325; VS_3047.
GeneIDi7162511.
KEGGivsp:VS_3047.
PATRICi20156606. VBIVibSpl48387_4235.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
FM954972 Genomic DNA. Translation: CAV20325.1 .
RefSeqi YP_002418565.1. NC_011753.2.

3D structure databases

ProteinModelPortali B7VMD4.
SMRi B7VMD4. Positions 4-272.
ModBasei Search...

Protein-protein interaction databases

STRINGi 575788.VS_3047.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAV20325 ; CAV20325 ; VS_3047 .
GeneIDi 7162511.
KEGGi vsp:VS_3047.
PATRICi 20156606. VBIVibSpl48387_4235.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci VSPL575788:GH64-2985-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. "Vibrio splendidus str. LGP32 complete genome."
    Mazel D., Le Roux F.
    Submitted (FEB-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LGP32.

Entry informationi

Entry nameiDAPF_VIBSL
AccessioniPrimary (citable) accession number: B7VMD4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: February 10, 2009
Last modified: June 11, 2014
This is version 38 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

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