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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leptospira borgpetersenii serovar Hardjo-bovis (strain L550)
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:iL-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

BioCyciLBOR355276:GHUQ-2993-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:LBL_3025
OrganismiLeptospira borgpetersenii serovar Hardjo-bovis (strain L550)
Taxonomic identifieri355276 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesLeptospiralesLeptospiraceaeLeptospira

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_1000011898Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi355276.LBL_3025.

Structurei

3D structure databases

ProteinModelPortaliQ04X60.
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

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMRIINSD.
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.

Q04X60-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAALKFTKME GIGNDYIYID STQANIRLTP EQIQKISNRN FGIGSDGVIF
60 70 80 90 100
IRNSKQGDFM MDMYNSDGSS SEMCGNGIRC VAKYIYDHGL TNSKNPKIET
110 120 130 140 150
GAGVLEVDLK IGSGNKVDFV SVNMGKPILV PSKIPVNWKD EEAIIDQTFE
160 170 180 190 200
IAGKNLKFTA VSMGNPHCVI FVDDCDQFPV TGIGPLIERH PIFPKRINVE
210 220 230 240 250
FVTVRGKDHF YQRTWERGAG ETLACGTGAC AVTVAGNLTG KSGKEVKIDL
260 270 280
RGGTLRIQWQ ESGNVLMTGP AKEIFSGEIE V
Length:281
Mass (Da):30,736
Last modified:November 14, 2006 - v1
Checksum:i08CB09F2D186D4EC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000348 Genomic DNA. Translation: ABJ80335.1.
RefSeqiWP_002727865.1. NC_008508.1.

Genome annotation databases

EnsemblBacteriaiABJ80335; ABJ80335; LBL_3025.
GeneIDi4405975.
KEGGilbl:LBL_3025.
PATRICi22370920. VBILepBor75619_3903.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000348 Genomic DNA. Translation: ABJ80335.1.
RefSeqiWP_002727865.1. NC_008508.1.

3D structure databases

ProteinModelPortaliQ04X60.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi355276.LBL_3025.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABJ80335; ABJ80335; LBL_3025.
GeneIDi4405975.
KEGGilbl:LBL_3025.
PATRICi22370920. VBILepBor75619_3903.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMRIINSD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciLBOR355276:GHUQ-2993-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: L550.

Entry informationi

Entry nameiDAPF_LEPBL
AccessioniPrimary (citable) accession number: Q04X60
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 14, 2006
Last modified: July 22, 2015
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.