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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rickettsia typhi (strain ATCC VR-144 / Wilmington)
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

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

  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

BioCyciRTYP257363:GJEQ-423-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:RT0401
OrganismiRickettsia typhi (strain ATCC VR-144 / Wilmington)
Taxonomic identifieri257363 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiatyphus group
ProteomesiUP000000604: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 270270Diaminopimelate epimerasePRO_0000278046Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi257363.RT0401.

Structurei

3D structure databases

ProteinModelPortaliQ68WW4.
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.
OMAiWMELIGN.
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.

Q68WW4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MINKINFVKM HGLGNDFVIV HKRDLATVCN LSQLAKNMAD RHTGIGCDQC
60 70 80 90 100
IIYEEYNNVY TMIIYNIDGS NAKLCGNATR CLAKLIYLDT GKKDITIMVG
110 120 130 140 150
KKKLLCNVEA ANKISVNVGN VSFNETWMPS RDRIWAFAER YMLDLKETMC
160 170 180 190 200
VDIGNPHLII FSKLEPQDQK IIGQKLQAKE LFVDGVNVNF AEVKDNKIYL
210 220 230 240 250
SVWERGAGLT LACGSGACGS FAAGLKLGFV HSPSTVVFKY GNLIMQEEDG
260 270
NIIMQGEATF VMRGEYYCEK
Length:270
Mass (Da):30,151
Last modified:October 11, 2004 - v1
Checksum:i3D6451DE36DCDC43
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017197 Genomic DNA. Translation: AAU03878.1.
RefSeqiYP_067360.1. NC_006142.1.

Genome annotation databases

EnsemblBacteriaiAAU03878; AAU03878; RT0401.
GeneIDi2959233.
KEGGirty:RT0401.
PATRICi17910036. VBIRicTyp34752_0430.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017197 Genomic DNA. Translation: AAU03878.1.
RefSeqiYP_067360.1. NC_006142.1.

3D structure databases

ProteinModelPortaliQ68WW4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi257363.RT0401.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAU03878; AAU03878; RT0401.
GeneIDi2959233.
KEGGirty:RT0401.
PATRICi17910036. VBIRicTyp34752_0430.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciRTYP257363:GJEQ-423-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC VR-144 / Wilmington.

Entry informationi

Entry nameiDAPF_RICTY
AccessioniPrimary (citable) accession number: Q68WW4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 20, 2007
Last sequence update: October 11, 2004
Last modified: January 7, 2015
This is version 63 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. Rickettsia typhi
    Rickettsia typhi (strain Wilmington): entries and gene names
  3. 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.