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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Clostridium perfringens (strain 13 / Type A)
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 sitei11SubstrateUniRule annotation1
Binding sitei63SubstrateUniRule annotation1
Active sitei72Proton donorUniRule annotation1
Sitei162Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei190SubstrateUniRule annotation1
Sitei208Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei217Proton 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:CPE1846
OrganismiClostridium perfringens (strain 13 / Type A)
Taxonomic identifieri195102 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium
Proteomesi
  • UP000000818 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498351 – 272Diaminopimelate epimeraseAdd BLAST272

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliQ46185.
SMRiQ46185.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni73 – 74Substrate bindingUniRule annotation2
Regioni208 – 209Substrate bindingUniRule annotation2
Regioni218 – 219Substrate 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.

Q46185-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFSKMHGNG NDFIVIEDLN NEYLGKEGEI AQKMCHRRFG IGADGILIVR
60 70 80 90 100
KNENCDIEMV IINSDGSYAA MCGNGIRCFA KYVYEKGIVK KDVLDVLTGD
110 120 130 140 150
GVKRIFLEIE NDKVKTINVN MGFGDFKPKN IPALCDEEII EKKVSVGNGN
160 170 180 190 200
FEITSLLMGV PHTIIFEEEK YPIECGRDIE KYELFPQGTN VNFCKVIDRN
210 220 230 240 250
TMEVRTWERG AGPTLACGTG NCASVIAANK LGLVDKEVKV IVPGGELKVN
260 270
IEDDGVKMIG NASFICDGTY LF
Length:272
Mass (Da):30,084
Last modified:January 31, 2002 - v2
Checksum:i60DB1A8527815C05
GO

Sequence cautioni

The sequence CAA60229 differs from that shown. Reason: Frameshift at position 181.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti183E → D in CAA60229 (PubMed:7559358).Curated1
Sequence conflicti193F → S in CAA60229 (PubMed:7559358).Curated1
Sequence conflicti201T → P in CAA60229 (PubMed:7559358).Curated1
Sequence conflicti206T → P in CAA60229 (PubMed:7559358).Curated1
Sequence conflicti230K → N in CAA60229 (PubMed:7559358).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000016 Genomic DNA. Translation: BAB81552.1.
X86511 Genomic DNA. Translation: CAA60229.1. Frameshift.
RefSeqiWP_011010638.1. NC_003366.1.

Genome annotation databases

EnsemblBacteriaiBAB81552; BAB81552; BAB81552.
KEGGicpe:CPE1846.
PATRICi19497647. VBICloPer59675_1919.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000016 Genomic DNA. Translation: BAB81552.1.
X86511 Genomic DNA. Translation: CAA60229.1. Frameshift.
RefSeqiWP_011010638.1. NC_003366.1.

3D structure databases

ProteinModelPortaliQ46185.
SMRiQ46185.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB81552; BAB81552; BAB81552.
KEGGicpe:CPE1846.
PATRICi19497647. VBICloPer59675_1919.

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_CLOPE
AccessioniPrimary (citable) accession number: Q46185
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 31, 2002
Last modified: March 15, 2017
This is version 108 of the entry and version 2 of the sequence. See 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

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.