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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Yersinia pestis
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 sitei11 – 111SubstrateUniRule annotation
Binding sitei44 – 441SubstrateUniRule annotation
Binding sitei64 – 641SubstrateUniRule annotation
Active sitei73 – 731Proton donor/acceptorUniRule annotation
Binding sitei157 – 1571SubstrateUniRule annotation
Sitei159 – 1591Important for catalytic activityUniRule annotation
Binding sitei190 – 1901SubstrateUniRule annotation
Sitei208 – 2081Important for catalytic activityUniRule annotation
Active sitei217 – 2171Proton 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

BioCyciYPES214092:GKDD-3816-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:YPO3845, y0385, YP_3202
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000000815: Chromosome, UP000001019: Chromosome, UP000002490: 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 – 274274Diaminopimelate epimerasePRO_0000149884Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi73 ↔ 217

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

IntActiP46357. 1 interaction.
STRINGi214092.YPO3845.

Structurei

3D structure databases

ProteinModelPortaliP46357.
SMRiP46357. Positions 1-274.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate bindingUniRule annotation
Regioni73 – 753Substrate bindingUniRule annotation
Regioni208 – 2092Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
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.

P46357-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFSKMHGLG NDFMVVDAVT QNVYFSPELI RRLADRHTGV GFDQMLVVEP
60 70 80 90 100
PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVRLKGLT NKREISVSTQ
110 120 130 140 150
TGRMILSVTE DEQVCVNMGE PDFEPQTVPF RAAKAEKTYI LRAAEHTVLC
160 170 180 190 200
GVVSMGNPHC VMQVDDVSVA NVALLGPVLE NHERFPERAN IGFMQVVSRD
210 220 230 240 250
HIRLRVYERG AGETQACGSG ACAAVAVGVV QDLLNENVHV ELPGGSLHIR
260 270
WQGPGHPLYM TGPATHVYDG FIHL
Length:274
Mass (Da):30,252
Last modified:November 16, 2001 - v2
Checksum:i8B66E79E67EB9FF1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti136 – 1361E → Q in AAC44326 (PubMed:8874804).Curated
Sequence conflicti186 – 19813PERAN…MQVVS → LSGQISALCRSSV in AAC44326 (PubMed:8874804).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22432.1.
AE009952 Genomic DNA. Translation: AAM83974.1.
AE017042 Genomic DNA. Translation: AAS63370.1.
U22968 Genomic DNA. Translation: AAC44326.1.
PIRiAE0468.
RefSeqiNP_667723.1. NC_004088.1.
NP_994493.1. NC_005810.1.
YP_002348723.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM83974; AAM83974; y0385.
AAS63370; AAS63370; YP_3202.
GeneIDi1145332.
1176680.
2765360.
KEGGiype:YPO3845.
ypk:y0385.
ypm:YP_3202.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22432.1.
AE009952 Genomic DNA. Translation: AAM83974.1.
AE017042 Genomic DNA. Translation: AAS63370.1.
U22968 Genomic DNA. Translation: AAC44326.1.
PIRiAE0468.
RefSeqiNP_667723.1. NC_004088.1.
NP_994493.1. NC_005810.1.
YP_002348723.1. NC_003143.1.

3D structure databases

ProteinModelPortaliP46357.
SMRiP46357. Positions 1-274.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP46357. 1 interaction.
STRINGi214092.YPO3845.

Protocols and materials databases

DNASUi1145332.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM83974; AAM83974; y0385.
AAS63370; AAS63370; YP_3202.
GeneIDi1145332.
1176680.
2765360.
KEGGiype:YPO3845.
ypk:y0385.
ypm:YP_3202.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciYPES214092:GKDD-3816-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

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CO-92 / Biovar Orientalis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KIM10+ / Biovar Mediaevalis.
  3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
    Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
    , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
    DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 91001 / Biovar Mediaevalis.
  4. "Comparative analysis of the cya locus in enterobacteria and related Gram-negative facultative anaerobes."
    Trotot P., Sismeiro O., Vivares C., Glaser P., Bresson-Roy A., Danchin A.
    Biochimie 78:277-287(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-198.
    Strain: EV 40.

Entry informationi

Entry nameiDAPF_YERPE
AccessioniPrimary (citable) accession number: P46357
Secondary accession number(s): Q0WAG5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 16, 2001
Last modified: January 7, 2015
This is version 110 of the entry and version 2 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

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.