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B9JUB9

- DAPF_AGRVS

UniProt

B9JUB9 - DAPF_AGRVS

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Agrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4))
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 sitei15 – 151SubstrateUniRule annotation
Binding sitei47 – 471SubstrateUniRule annotation
Binding sitei67 – 671SubstrateUniRule annotation
Active sitei76 – 761Proton donor/acceptorUniRule annotation
Binding sitei163 – 1631SubstrateUniRule annotation
Sitei165 – 1651Important for catalytic activityUniRule annotation
Binding sitei197 – 1971SubstrateUniRule annotation
Sitei215 – 2151Important for catalytic activityUniRule annotation
Active sitei224 – 2241Proton 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

BioCyciAVIT311402:GH2Y-3159-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:Avi_4198
OrganismiAgrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4))
Taxonomic identifieri311402 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacterium
ProteomesiUP000001596: Chromosome 1

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 – 303303Diaminopimelate epimerasePRO_1000124397Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 224

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi311402.Avi_4198.

Structurei

3D structure databases

ProteinModelPortaliB9JUB9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni12 – 132Substrate bindingUniRule annotation
Regioni76 – 783Substrate bindingUniRule annotation
Regioni215 – 2162Substrate 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.

B9JUB9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGNRVEFAKM NGLGNKILVV DMRGRADRVM PQAAIALAGN AETHFDQIMA
60 70 80 90 100
IHDPKLAGTF AYIDIINCDG TLAQACGNGT RCVVQALSAE TGLKAFTFQT
110 120 130 140 150
LAGILNAVEH DDRTVSVDMG SPVFDWNRIP LSEEFHDTSR IELQIGPIDA
160 170 180 190 200
PVLHSPAVMS MGNPHAVFWV DRDPMSYDLE RFGPLLENHP LFPEKANITL
210 220 230 240 250
AQVTSRTTMT TRTWERGAGL TLACGSAACA AGVSAARTGR AERKVTITVA
260 270 280 290 300
SSPNRQALDI EWRERDGHVI MTGAAEWEWA GQLDPQTGDW QREQQAGHEA

SVS
Length:303
Mass (Da):32,938
Last modified:March 24, 2009 - v1
Checksum:i576CE7C264678232
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000633 Genomic DNA. Translation: ACM38042.1.
RefSeqiYP_002551054.1. NC_011989.1.

Genome annotation databases

EnsemblBacteriaiACM38042; ACM38042; Avi_4198.
GeneIDi7386963.
KEGGiavi:Avi_4198.
PATRICi20831920. VBIAgrVit37146_5599.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000633 Genomic DNA. Translation: ACM38042.1 .
RefSeqi YP_002551054.1. NC_011989.1.

3D structure databases

ProteinModelPortali B9JUB9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 311402.Avi_4198.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACM38042 ; ACM38042 ; Avi_4198 .
GeneIDi 7386963.
KEGGi avi:Avi_4198.
PATRICi 20831920. VBIAgrVit37146_5599.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci AVIT311402:GH2Y-3159-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S4 / ATCC BAA-846.

Entry informationi

Entry nameiDAPF_AGRVS
AccessioniPrimary (citable) accession number: B9JUB9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: October 29, 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, 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