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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rickettsia canadensis (strain McKiel)
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

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei15 – 151SubstrateUniRule annotation
Binding sitei49 – 491SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei75 – 751Proton donor/acceptorUniRule annotation
Binding sitei155 – 1551SubstrateUniRule annotation
Sitei157 – 1571Important for catalytic activityUniRule annotation
Binding sitei187 – 1871SubstrateUniRule annotation
Sitei204 – 2041Important for catalytic activityUniRule annotation
Active sitei213 – 2131Proton donor/acceptorUniRule annotation

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

BioCyciRCAN293613:GHI3-659-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:A1E_03280
OrganismiRickettsia canadensis (strain McKiel)
Taxonomic identifieri293613 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiabelli group
ProteomesiUP000007056 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 269269Diaminopimelate epimerasePRO_1000011954Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 213

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi293613.A1E_03280.

Structurei

3D structure databases

ProteinModelPortaliA8EZ08.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni12 – 132Substrate bindingUniRule annotation
Regioni75 – 773Substrate bindingUniRule annotation
Regioni204 – 2052Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLCRIEDE.
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.

A8EZ08-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MISKINFVKM HGLGNDCVIV NKRDLLNAHN LSQLAKNIAD RHTGIGCDQF
60 70 80 90 100
IIYENHNNFY EMIIYNIDGS SAKLCGNATR CLAKLIYLDT GKKDITIVVG
110 120 130 140 150
NKELLCRIED ENKISVNVGA VSFNETWMPS RDKIWAFAAR YMIDLKETIC
160 170 180 190 200
VDVGNPHLVI FSKLESQDQK IVGETLQAKE LFANGVNVNF AEIKDNKINL
210 220 230 240 250
SVWERGVGLT GACGSGACGS FAAGLKRGFI HSPSTVVFKH GSLNMKEENG
260
NIIMQGSATL IAEGVYCCE
Length:269
Mass (Da):29,584
Last modified:November 13, 2007 - v1
Checksum:i68A1E6E4A062CE9F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000409 Genomic DNA. Translation: ABV73591.1.
RefSeqiWP_012148787.1. NC_009879.1.
YP_001492376.1. NC_009879.1.

Genome annotation databases

EnsemblBacteriaiABV73591; ABV73591; A1E_03280.
KEGGircm:A1E_03280.
PATRICi17885985. VBIRicCan89738_0702.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000409 Genomic DNA. Translation: ABV73591.1.
RefSeqiWP_012148787.1. NC_009879.1.
YP_001492376.1. NC_009879.1.

3D structure databases

ProteinModelPortaliA8EZ08.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi293613.A1E_03280.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABV73591; ABV73591; A1E_03280.
KEGGircm:A1E_03280.
PATRICi17885985. VBIRicCan89738_0702.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLCRIEDE.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciRCAN293613:GHI3-659-MONOMER.

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]
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of Rickettsia canadensis."
    Madan A., Fahey J., Helton E., Ketteman M., Madan A., Rodrigues S., Sanchez A., Whiting M., Dasch G., Eremeeva M.
    Submitted (SEP-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: McKiel.

Entry informationi

Entry nameiDAPF_RICCK
AccessioniPrimary (citable) accession number: A8EZ08
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 13, 2007
Last modified: April 29, 2015
This is version 48 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

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 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.