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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodococcus erythropolis (strain PR4 / NBRC 100887)
Status
Reviewed-Annotation score: 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: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei14SubstrateUniRule annotation1
Binding sitei47SubstrateUniRule annotation1
Binding sitei81SubstrateUniRule annotation1
Active sitei90Proton donor/acceptorUniRule annotation1
Binding sitei166SubstrateUniRule annotation1
Sitei168Important for catalytic activityUniRule annotation1
Binding sitei202SubstrateUniRule annotation1
Sitei220Important for catalytic activityUniRule annotation1
Active sitei229Proton donor/acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

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:RER_27650
OrganismiRhodococcus erythropolis (strain PR4 / NBRC 100887)
Taxonomic identifieri234621 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000002204 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10002040651 – 292Diaminopimelate epimeraseAdd BLAST292

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi90 ↔ 229

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi234621.RER_27650.

Structurei

3D structure databases

ProteinModelPortaliC0ZYN8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni90 – 92Substrate bindingUniRule annotation3
Regioni220 – 221Substrate bindingUniRule annotation2
Regioni230 – 231Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
KOiK01778.
OMAiTKGHGTQ.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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.

C0ZYN8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATMDFSKGH GTQNDFVVLP DLDVRVDLEP ARVSALCDRQ RGLGADGILR
60 70 80 90 100
VARAGALADA GVLGALPDGV AAEDWFMDYR NSDGSIAEMC GNGVRVFAHY
110 120 130 140 150
LKASGLESKD EFVVGSRAGA RPVVVHGYDA THGDVTVAMG PIKDLGTSSA
160 170 180 190 200
TIDGRVFAGV GIDVGNPHLA CVDEHVTAEV LSALDLSVSP GFDPGFFPHG
210 220 230 240 250
VNIEIVTPIH DGGVHMRVHE RGVGETRSCG TGTVAAAAAA LKFDGRDEGS
260 270 280 290
VLVRVLGGEV QVTVEGGEGS LRGPSVLVAN GTISDAWWQS LV
Length:292
Mass (Da):30,225
Last modified:May 26, 2009 - v1
Checksum:i04394249808533A9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008957 Genomic DNA. Translation: BAH33473.1.

Genome annotation databases

EnsemblBacteriaiBAH33473; BAH33473; RER_27650.
KEGGirer:RER_27650.
PATRICi23191930. VBIRhoEry66701_3256.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008957 Genomic DNA. Translation: BAH33473.1.

3D structure databases

ProteinModelPortaliC0ZYN8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi234621.RER_27650.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAH33473; BAH33473; RER_27650.
KEGGirer:RER_27650.
PATRICi23191930. VBIRhoEry66701_3256.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
KOiK01778.
OMAiTKGHGTQ.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_RHOE4
AccessioniPrimary (citable) accession number: C0ZYN8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: May 26, 2009
Last modified: November 2, 2016
This is version 54 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.