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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leptospira biflexa serovar Patoc (strain Patoc 1 / Ames)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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: 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)DescriptionActionsGraphical viewLength
Binding sitei13SubstrateUniRule annotation1
Binding sitei64SubstrateUniRule annotation1
Active sitei73Proton donorUniRule annotation1
Binding sitei164SubstrateUniRule annotation1
Sitei166Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Sitei215Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei224Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Alternative name(s):
PLP-independent amino acid racemaseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:LBF_0565
OrganismiLeptospira biflexa serovar Patoc (strain Patoc 1 / Ames)
Taxonomic identifieri355278 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesLeptospiralesLeptospiraceaeLeptospira

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001186731 – 280Diaminopimelate epimeraseAdd BLAST280

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliB0SC36.
SMRiB0SC36.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni74 – 75Substrate bindingUniRule annotation2
Regioni215 – 216Substrate bindingUniRule annotation2
Regioni225 – 226Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiView protein in PROSITE
PS01326. DAP_EPIMERASE. 1 hit.

Sequencei

Sequence statusi: Complete.

B0SC36-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKINFTKMEG IGNDYVYIDA TKNDIRLSPE QIQKLSDRNF GIGGDGVIFI
60 70 80 90 100
RNSNSGEFQM DMYNSDGSSS EMCGNGVRCV GKFVYDHGLT KNQKPTIETG
110 120 130 140 150
KGVLTLDLKT GTNGKVEMVT VDMGEPILKP SLVPIVWKGD EPVINQVIEV
160 170 180 190 200
QGKQYHFTAV SMGNPHCVIY VDDADDFPVR EIGPIIENHP FFPRRVNVEF
210 220 230 240 250
VSIKGKDHLY QRTWERGTGE TLACGTGACA VTVASILNGK TGRSVRIDLR
260 270 280
GGTLHIEWQE NGSVFMTGPA KEVFSGEVEI
Length:280
Mass (Da):30,826
Last modified:April 8, 2008 - v1
Checksum:i05DE546E3D9C2CC6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000777 Genomic DNA. Translation: ABZ93101.1.
RefSeqiWP_012476131.1. NC_010842.1.

Genome annotation databases

EnsemblBacteriaiABZ93101; ABZ93101; LBF_0565.
KEGGilbf:LBF_0565.
PATRICi22340035. VBILepBif95142_0592.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000777 Genomic DNA. Translation: ABZ93101.1.
RefSeqiWP_012476131.1. NC_010842.1.

3D structure databases

ProteinModelPortaliB0SC36.
SMRiB0SC36.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABZ93101; ABZ93101; LBF_0565.
KEGGilbf:LBF_0565.
PATRICi22340035. VBILepBif95142_0592.

Phylogenomic databases

HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiView protein in PROSITE
PS01326. DAP_EPIMERASE. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_LEPBA
AccessioniPrimary (citable) accession number: B0SC36
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: April 8, 2008
Last modified: March 15, 2017
This is version 61 of the entry and version 1 of the sequence. See 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

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 one 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.