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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060)
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 sitei42 – 421SubstrateUniRule annotation
Binding sitei60 – 601SubstrateUniRule annotation
Active sitei69 – 691Proton donor/acceptorUniRule annotation
Sitei138 – 1381Important for catalytic activityUniRule annotation
Binding sitei164 – 1641SubstrateUniRule annotation
Sitei182 – 1821Important for catalytic activityUniRule annotation
Active sitei192 – 1921Proton 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

BioCyciCLAR306263:GH7X-54-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:Cla_0054
OrganismiCampylobacter lari (strain RM2100 / D67 / ATCC BAA-1060)
Taxonomic identifieri306263 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesCampylobacteraceaeCampylobacter
ProteomesiUP000007727 Componenti: 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 – 249249Diaminopimelate epimerasePRO_1000124405Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi69 ↔ 192

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi306263.Cla_0054.

Structurei

3D structure databases

ProteinModelPortaliB9KED6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni69 – 713Substrate bindingUniRule annotation
Regioni182 – 1832Substrate bindingUniRule annotation
Regioni193 – 1942Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
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.

B9KED6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFYKYCASG NDFVIFADSE KKDRSELAKI LCNRYEGIGA DGLIVIVPHD
60 70 80 90 100
RYDFEWEFYN CDGSKANMCG NGSRAAAHFA HHHLKKSQYL NFLTGAGLIK
110 120 130 140 150
SFVDDDIVEI KLSGIKDIKE AFEYKDRIWQ GCNTGVPHIV TFVDDLSEFD
160 170 180 190 200
INLCKEVRKK YNANVNFAKV EDDEFIRVRT YERGVEDETL ACGTGMGACF
210 220 230 240
YLAYLNQKVK DDILIKPKSN ESLYFRLEEE QIFFRGKVKC CFEADYNFT
Length:249
Mass (Da):28,688
Last modified:March 24, 2009 - v1
Checksum:i3DD123F7A4E7280F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000932 Genomic DNA. Translation: ACM63421.1.
RefSeqiYP_002574672.1. NC_012039.1.

Genome annotation databases

EnsemblBacteriaiACM63421; ACM63421; Cla_0054.
KEGGicla:Cla_0054.
PATRICi20060549. VBICamLar15090_0054.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000932 Genomic DNA. Translation: ACM63421.1.
RefSeqiYP_002574672.1. NC_012039.1.

3D structure databases

ProteinModelPortaliB9KED6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi306263.Cla_0054.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACM63421; ACM63421; Cla_0054.
KEGGicla:Cla_0054.
PATRICi20060549. VBICamLar15090_0054.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiHEGFGAD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCLAR306263:GH7X-54-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. "The complete genome sequence and analysis of the human pathogen Campylobacter lari."
    Miller W.G., Wang G., Binnewies T.T., Parker C.T.
    Foodborne Pathog. Dis. 5:371-386(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RM2100 / D67 / ATCC BAA-1060.

Entry informationi

Entry nameiDAPF_CAMLR
AccessioniPrimary (citable) accession number: B9KED6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: April 1, 2015
This is version 44 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.