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C5CND4

- DAPF_VARPS

UniProt

C5CND4 - DAPF_VARPS

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Protein
Diaminopimelate epimerase
Gene
dapF, Vapar_0899
Organism
Variovorax paradoxus (strain S110)
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 sitei69 – 691Substrate By similarity
Active sitei78 – 781Proton donor/acceptor By similarity
Binding sitei173 – 1731Substrate By similarity
Sitei175 – 1751Important for catalytic activity By similarity
Binding sitei206 – 2061Substrate By similarity
Sitei224 – 2241Important for catalytic activity By similarity
Active sitei233 – 2331Proton 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

BioCyciVPAR543728:GHLL-906-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:Vapar_0899
OrganismiVariovorax paradoxus (strain S110)
Taxonomic identifieri543728 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
ProteomesiUP000000453: 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 – 294294Diaminopimelate epimeraseUniRule annotation
PRO_1000204070Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi78 ↔ 233UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi543728.Vapar_0899.

Structurei

3D structure databases

ProteinModelPortaliC5CND4.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni78 – 803Substrate binding By similarity
Regioni224 – 2252Substrate binding By similarity
Regioni234 – 2352Substrate 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.

C5CND4-1 [UniParc]FASTAAdd to Basket

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MRIRFTKMQG AGNDFVVLDE TRGTLGLTAA QYRFLADRHF GVGADQILTV    50
RPPSKGAAEG VDFQYVIHNA DGGEVEQCGN GARCFMRFVR EHHLTDKDTV 100
RVETLAGIIE PRMGADGRVT VDMGPPIFEP ARVPFDTAGL DPQPTGSWHT 150
WHLALGTHAD SAIVSVAVLS MGNPHAVQVV DNVDTAPVAR QGPLIEHHPR 200
FAQRVNAGFM QVVDRSHIKL RVFERGAGET LACGTGACAA VVAGIRLGLL 250
ERRVDVQTHG GVLTIGWEGE GHPVLMTGPA TTVFEGDIEV PELP 294
Length:294
Mass (Da):31,618
Last modified:July 28, 2009 - v1
Checksum:i5279A4320AD6A5F4
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001635 Genomic DNA. Translation: ACS17550.1.
RefSeqiYP_002942816.1. NC_012791.1.

Genome annotation databases

EnsemblBacteriaiACS17550; ACS17550; Vapar_0899.
GeneIDi7970074.
KEGGivap:Vapar_0899.
PATRICi24002200. VBIVarPar36677_0909.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001635 Genomic DNA. Translation: ACS17550.1 .
RefSeqi YP_002942816.1. NC_012791.1.

3D structure databases

ProteinModelPortali C5CND4.
ModBasei Search...

Protein-protein interaction databases

STRINGi 543728.Vapar_0899.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACS17550 ; ACS17550 ; Vapar_0899 .
GeneIDi 7970074.
KEGGi vap:Vapar_0899.
PATRICi 24002200. VBIVarPar36677_0909.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci VPAR543728:GHLL-906-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 metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110."
    Han J.I., Choi H.K., Lee S.W., Orwin P.M., Kim J., Laroe S.L., Kim T.G., O'Neil J., Leadbetter J.R., Lee S.Y., Hur C.G., Spain J.C., Ovchinnikova G., Goodwin L., Han C.
    J. Bacteriol. 193:1183-1190(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S110.

Entry informationi

Entry nameiDAPF_VARPS
AccessioniPrimary (citable) accession number: C5CND4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: June 11, 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

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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