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C1B393

- DAPF_RHOOB

UniProt

C1B393 - DAPF_RHOOB

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodococcus opacus (strain B4)
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 sitei11 – 111SubstrateUniRule annotation
Binding sitei44 – 441SubstrateUniRule annotation
Binding sitei78 – 781SubstrateUniRule annotation
Active sitei87 – 871Proton donor/acceptorUniRule annotation
Binding sitei163 – 1631SubstrateUniRule annotation
Sitei165 – 1651Important for catalytic activityUniRule annotation
Binding sitei199 – 1991SubstrateUniRule annotation
Sitei217 – 2171Important for catalytic activityUniRule annotation
Active sitei226 – 2261Proton 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

BioCyciROPA632772:GH0Q-6813-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:ROP_67630
OrganismiRhodococcus opacus (strain B4)
Taxonomic identifieri632772 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeRhodococcus
ProteomesiUP000002212: 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 – 289289Diaminopimelate epimerasePRO_1000124430Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi87 ↔ 226

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi632772.ROP_67630.

Structurei

3D structure databases

ProteinModelPortaliC1B393.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 893Substrate bindingUniRule annotation
Regioni217 – 2182Substrate bindingUniRule annotation
Regioni227 – 2282Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiITIEMGT.
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.

C1B393-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDFSKGHGTE NDFVVLPDPD VRIDLSAPRV AALCDRRRGL GADGILRVAK
60 70 80 90 100
AGALAAAGVL AELPDGTSED DWFMDYRNAD GSIAEMCGNG VRVFAHYLRS
110 120 130 140 150
TGLETRDEFV VGSRAGGKPV IVHSADGSAG EVTVDMGVVR DLGTSAATID
160 170 180 190 200
GKVFNGIGID VGNPHLACVD AHLTAASLSA LDLTAAPGFD PGFFPHGVNV
210 220 230 240 250
EILTRIDSGA VDMRVHERGV GETRSCGTGT VAAATAALRF DGADSGEVKV
260 270 280
RIPGGQVTVA LSGGRATLRG PSVLVASGNL DDSWWNGLS
Length:289
Mass (Da):29,725
Last modified:May 26, 2009 - v1
Checksum:i01ED7A2C9E5309E7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP011115 Genomic DNA. Translation: BAH55010.1.
RefSeqiYP_002783955.1. NC_012522.1.

Genome annotation databases

EnsemblBacteriaiBAH55010; BAH55010; ROP_67630.
GeneIDi7745421.
KEGGirop:ROP_67630.
PATRICi23230959. VBIRhoOpa21106_6844.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP011115 Genomic DNA. Translation: BAH55010.1 .
RefSeqi YP_002783955.1. NC_012522.1.

3D structure databases

ProteinModelPortali C1B393.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 632772.ROP_67630.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAH55010 ; BAH55010 ; ROP_67630 .
GeneIDi 7745421.
KEGGi rop:ROP_67630.
PATRICi 23230959. VBIRhoOpa21106_6844.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220467.
KOi K01778.
OMAi ITIEMGT.
OrthoDBi EOG6ND0M5.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci ROPA632772:GH0Q-6813-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. "Comparison of the complete genome sequences of Rhodococcus erythropolis PR4 and Rhodococcus opacus B4."
    Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S., Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.
    Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: B4.

Entry informationi

Entry nameiDAPF_RHOOB
AccessioniPrimary (citable) accession number: C1B393
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3