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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / NCTC 11154)
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 sitei163 – 1631SubstrateUniRule annotation
Sitei165 – 1651Important for catalytic activityUniRule annotation
Binding sitei196 – 1961SubstrateUniRule annotation
Sitei214 – 2141Important for catalytic activityUniRule annotation
Active sitei223 – 2231Proton 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

BioCyciBVUL435590:GH96-3996-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:BVU_4006
OrganismiBacteroides vulgatus (strain ATCC 8482 / DSM 1447 / NCTC 11154)
Taxonomic identifieri435590 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesBacteroidaceaeBacteroides
ProteomesiUP000002861: 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 – 280280Diaminopimelate epimerasePRO_1000011844Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi75 ↔ 223

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi435590.BVU_4006.

Structurei

3D structure databases

ProteinModelPortaliA6L7E5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 773Substrate bindingUniRule annotation
Regioni214 – 2152Substrate bindingUniRule annotation
Regioni224 – 2252Substrate 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.

A6L7E5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MATTIKFTKM QGTGNDYIYV NTLSSPLQDP IKAARKWSTY HTGIGADGLV
60 70 80 90 100
LIGASEKADF SMRIFNADGS EAMMCGNASR CIGKYVYEKG LTDKEVITLE
110 120 130 140 150
TLSGIKILKL HTGNGVVKDV TVDMGTPLLS NPGQIATKTG GMLAETIPAD
160 170 180 190 200
GKEYKGTFVC MGNPHVVIFV DDIKEVDLPA VGPKLENHPL FPERTNVEFV
210 220 230 240 250
EILPDQSLRM RVWERGSGIT MACGTGACAT AVAAVLNHKA GRKSWVRMDG
260 270 280
GDLHIHWNEK DGHVYMTGPA GKVFEGEIEM
Length:280
Mass (Da):30,295
Last modified:July 24, 2007 - v1
Checksum:i250E887C76250C39
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000139 Genomic DNA. Translation: ABR41609.1.
RefSeqiWP_005839633.1. NC_009614.1.
YP_001301231.1. NC_009614.1.

Genome annotation databases

EnsemblBacteriaiABR41609; ABR41609; BVU_4006.
GeneIDi5304965.
KEGGibvu:BVU_4006.
PATRICi21073106. VBIBacVul85104_4115.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000139 Genomic DNA. Translation: ABR41609.1.
RefSeqiWP_005839633.1. NC_009614.1.
YP_001301231.1. NC_009614.1.

3D structure databases

ProteinModelPortaliA6L7E5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi435590.BVU_4006.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR41609; ABR41609; BVU_4006.
GeneIDi5304965.
KEGGibvu:BVU_4006.
PATRICi21073106. VBIBacVul85104_4115.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciBVUL435590:GH96-3996-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 8482 / DSM 1447 / NCTC 11154.

Entry informationi

Entry nameiDAPF_BACV8
AccessioniPrimary (citable) accession number: A6L7E5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 24, 2007
Last modified: January 7, 2015
This is version 51 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.