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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
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 sitei14 – 141SubstrateUniRule annotation
Binding sitei47 – 471SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei165 – 1651SubstrateUniRule annotation
Sitei167 – 1671Important for catalytic activityUniRule annotation
Binding sitei198 – 1981SubstrateUniRule annotation
Sitei216 – 2161Important for catalytic activityUniRule annotation
Active sitei225 – 2251Proton 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

BioCyciLINT267671:GHQI-74-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:LIC_10074
OrganismiLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
Taxonomic identifieri267671 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesLeptospiralesLeptospiraceaeLeptospira
ProteomesiUP000007037 Componenti: Chromosome I

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 – 281281Diaminopimelate epimerasePRO_0000149847Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 225

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi267671.LIC10074.

Structurei

3D structure databases

ProteinModelPortaliQ72W63.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 122Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni216 – 2172Substrate bindingUniRule annotation
Regioni226 – 2272Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

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.

Q72W63-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASLKFTKME GIGNDYVYID STRNDIRLTP EQIQKISDRN FGIGSDGVIF
60 70 80 90 100
IRNSKQGDFM MDMYNSDGSS SEMCGNGIRC VAKYIYDHGL TSSKNPKIET
110 120 130 140 150
GAGILEVDLK IGSGNKVDLV SVDMGKPVLV PSQIPVVWKN EETIIDQPLE
160 170 180 190 200
IGDKNLKFTA VSMGNPHCVI FVDDSDEFPV RGIGPLIERH SIFPKRVNVE
210 220 230 240 250
FVTIRGKDHL YQRTWERGAG ETLACGTGAC AVMVAGNLTG RSGKDVQIDL
260 270 280
RGGTLRIQWQ ESGNILMTGP AREIFSGEIE I
Length:281
Mass (Da):30,867
Last modified:July 5, 2004 - v1
Checksum:iDBFDCC0E72DE1151
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016823 Genomic DNA. Translation: AAS68711.1.
RefSeqiWP_000157608.1. NC_005823.1.
YP_000074.1. NC_005823.1.

Genome annotation databases

EnsemblBacteriaiAAS68711; AAS68711; LIC_10074.
KEGGilic:LIC10074.
PATRICi22371808. VBILepInt6257_0086.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016823 Genomic DNA. Translation: AAS68711.1.
RefSeqiWP_000157608.1. NC_005823.1.
YP_000074.1. NC_005823.1.

3D structure databases

ProteinModelPortaliQ72W63.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi267671.LIC10074.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS68711; AAS68711; LIC_10074.
KEGGilic:LIC10074.
PATRICi22371808. VBILepInt6257_0086.

Phylogenomic databases

KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciLINT267671:GHQI-74-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. "Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis."
    Nascimento A.L.T.O., Ko A.I., Martins E.A.L., Monteiro-Vitorello C.B., Ho P.L., Haake D.A., Verjovski-Almeida S., Hartskeerl R.A., Marques M.V., Oliveira M.C., Menck C.F.M., Leite L.C.C., Carrer H., Coutinho L.L., Degrave W.M., Dellagostin O.A., El-Dorry H., Ferro E.S.
    , Ferro M.I.T., Furlan L.R., Gamberini M., Giglioti E.A., Goes-Neto A., Goldman G.H., Goldman M.H.S., Harakava R., Jeronimo S.M.B., Junqueira-de-Azevedo I.L.M., Kimura E.T., Kuramae E.E., Lemos E.G.M., Lemos M.V.F., Marino C.L., Nunes L.R., de Oliveira R.C., Pereira G.G., Reis M.S., Schriefer A., Siqueira W.J., Sommer P., Tsai S.M., Simpson A.J.G., Ferro J.A., Camargo L.E.A., Kitajima J.P., Setubal J.C., Van Sluys M.A.
    J. Bacteriol. 186:2164-2172(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Fiocruz L1-130.

Entry informationi

Entry nameiDAPF_LEPIC
AccessioniPrimary (citable) accession number: Q72W63
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: July 5, 2004
Last modified: June 24, 2015
This is version 72 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.