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B9JCL3

- DAPF_AGRRK

UniProt

B9JCL3 - DAPF_AGRRK

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Agrobacterium radiobacter (strain K84 / ATCC BAA-868)
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

BioCyciARAD311403:GHU8-3423-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:Arad_4405
OrganismiAgrobacterium radiobacter (strain K84 / ATCC BAA-868)
Taxonomic identifieri311403 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
ProteomesiUP000001600: 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 – 301301Diaminopimelate epimerasePRO_1000124396Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi311403.Arad_4405.

Structurei

3D structure databases

ProteinModelPortaliB9JCL3.
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.
OMAiRPAENGA.
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.

B9JCL3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSNTVEFARM NGLGNKILVV DMRGRKDVVT AAAAIALNAD PATEFDQIMA
60 70 80 90 100
IHDPKAEGTD AWIDILNSDG TKAQACGNGT RCVVQALAAE TGKKVFTFQT
110 120 130 140 150
VAGILNAVEH EDGTISVDMG RPVFDWDKIP LAEEFADTRR IELQIGPIDN
160 170 180 190 200
PVLHSPSVMS MGNPHAIFWV DKDPMSYDLA RFGPLLENHP MFPERANITL
210 220 230 240 250
AQVLSPTLLR TRTWERGAGL TLACGSAACS AAVSAARTGR TGRKVTIDVA
260 270 280 290 300
SAPASGQLTI EWRENDDHVV MTGPAEWEWS GVVDPVTGSF TRAQEQGAQA

R
Length:301
Mass (Da):32,398
Last modified:March 24, 2009 - v1
Checksum:iC383F5433B5F4D0B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000628 Genomic DNA. Translation: ACM28124.1.
RefSeqiWP_012652711.1. NC_011985.1.
YP_002546057.1. NC_011985.1.

Genome annotation databases

EnsemblBacteriaiACM28124; ACM28124; Arad_4405.
GeneIDi7371437.
KEGGiara:Arad_4405.
PATRICi20807728. VBIAgrRad129173_5931.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000628 Genomic DNA. Translation: ACM28124.1 .
RefSeqi WP_012652711.1. NC_011985.1.
YP_002546057.1. NC_011985.1.

3D structure databases

ProteinModelPortali B9JCL3.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 311403.Arad_4405.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACM28124 ; ACM28124 ; Arad_4405 .
GeneIDi 7371437.
KEGGi ara:Arad_4405.
PATRICi 20807728. VBIAgrRad129173_5931.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci ARAD311403:GHU8-3423-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: K84 / ATCC BAA-868.

Entry informationi

Entry nameiDAPF_AGRRK
AccessioniPrimary (citable) accession number: B9JCL3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: October 29, 2014
This is version 40 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