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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / NCTC 11152)
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 sitei15 – 151SubstrateUniRule annotation
Binding sitei48 – 481SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei75 – 751Proton donor/acceptorUniRule annotation
Binding sitei152 – 1521SubstrateUniRule annotation
Sitei154 – 1541Important for catalytic activityUniRule annotation
Binding sitei185 – 1851SubstrateUniRule annotation
Sitei203 – 2031Important for catalytic activityUniRule annotation
Active sitei212 – 2121Proton 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

BioCyciPDIS435591:GCNH-322-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:BDI_0322
OrganismiParabacteroides distasonis (strain ATCC 8503 / DSM 20701 / NCTC 11152)
Taxonomic identifieri435591 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaeParabacteroides
ProteomesiUP000000566: 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 – 269269Diaminopimelate epimerasePRO_1000011922Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 212

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi435591.BDI_0322.

Structurei

3D structure databases

ProteinModelPortaliA6L8U3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 773Substrate bindingUniRule annotation
Regioni203 – 2042Substrate bindingUniRule annotation
Regioni213 – 2142Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
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.

A6L8U3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKSIRFTKM HGAGNDYIYV NTMAYPIDNP EELSIAWSKP HTGIGSDGLV
60 70 80 90 100
LIGSSDIADF SMHIYNADGS EAMMCGNASR CIGKYVYEAG LTQKNKVTLE
110 120 130 140 150
TLSGIKELQL KIEREEVTEV TVDMGMPAVG EMALEVEAGG EIYTGTVISM
160 170 180 190 200
GNPHLVIFVD EMDQVGLASV GPLLECLPLF PDRTNVEFVQ VLKPDEVRMR
210 220 230 240 250
VWERGSGITQ ACGTGACATA VAGVVRGKTK RKTKVIMDGG PLTIEWDERS
260
GKVFMTGGAV NVFEGFIKV
Length:269
Mass (Da):29,082
Last modified:July 24, 2007 - v1
Checksum:i5D9FC2F04DDA055F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000140 Genomic DNA. Translation: ABR42107.1.
RefSeqiWP_011965968.1. NC_009615.1.
YP_001301729.1. NC_009615.1.

Genome annotation databases

EnsemblBacteriaiABR42107; ABR42107; BDI_0322.
GeneIDi5305477.
KEGGipdi:BDI_0322.
PATRICi22843794. VBIParDis29947_0318.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000140 Genomic DNA. Translation: ABR42107.1.
RefSeqiWP_011965968.1. NC_009615.1.
YP_001301729.1. NC_009615.1.

3D structure databases

ProteinModelPortaliA6L8U3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi435591.BDI_0322.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR42107; ABR42107; BDI_0322.
GeneIDi5305477.
KEGGipdi:BDI_0322.
PATRICi22843794. VBIParDis29947_0318.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciPDIS435591:GCNH-322-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: ATCC 8503 / DSM 20701 / NCTC 11152.

Entry informationi

Entry nameiDAPF_PARD8
AccessioniPrimary (citable) accession number: A6L8U3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 24, 2007
Last modified: March 4, 2015
This is version 55 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, Reference 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.