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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Uncultured methanogenic archaeon RC-I
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.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei14 – 141SubstrateUniRule annotation
Binding sitei49 – 491SubstrateUniRule annotation
Binding sitei67 – 671SubstrateUniRule annotation
Active sitei76 – 761Proton donor/acceptorUniRule annotation
Sitei161 – 1611Important for catalytic activityUniRule annotation
Binding sitei193 – 1931SubstrateUniRule annotation
Sitei210 – 2101Important for catalytic activityUniRule annotation
Active sitei220 – 2201Proton 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

BioCyciUMET351160:GJT4-1146-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:UNCMA_11190
ORF Names:RCIX1964
OrganismiUncultured methanogenic archaeon RC-I
Taxonomic identifieri351160 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanomicrobiaMethanocellalesMethanocellaceaeMethanocella
ProteomesiUP000000663: 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_1000011979Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 220

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi351160.RCIX1964.

Structurei

3D structure databases

ProteinModelPortaliQ0W3B6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni76 – 783Substrate bindingUniRule annotation
Regioni210 – 2112Substrate bindingUniRule annotation
Regioni221 – 2222Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.

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.

Q0W3B6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKIKFTKMH GNGNDFIVID EFENPVPEEK KAAFAKKVCH RRFGIGADGV
60 70 80 90 100
LFLAKPLHTS LHMRIFNEDG SEAEMCGNGI RCFVKYAVDN GHMNPGKDKV
110 120 130 140 150
ETKAGILEVE ARIEDGKTLV KVSMGKPLFD PKKIPAAGLN NFINKPLHGY
160 170 180 190 200
EVTAVNTGVP HAVIFVDDVN AVDLMKVAPE IRYDLKTFPK GINVNFVQRE
210 220 230 240 250
GHNLRVRTYE RGVEGETLSC GTGSVASAAV ARYLGYTRDE TTVYTAGGQL
260 270 280
NISFVSDIAY MEGPAETVYE GEIDVDFSAL
Length:280
Mass (Da):30,722
Last modified:September 5, 2006 - v1
Checksum:i3DE0C9B952CFC360
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM114193 Genomic DNA. Translation: CAJ37127.1.
RefSeqiYP_686453.1. NC_009464.1.

Genome annotation databases

EnsemblBacteriaiCAJ37127; CAJ37127; RCIX1964.
GeneIDi5144870.
KEGGirci:RCIX1964.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM114193 Genomic DNA. Translation: CAJ37127.1.
RefSeqiYP_686453.1. NC_009464.1.

3D structure databases

ProteinModelPortaliQ0W3B6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi351160.RCIX1964.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAJ37127; CAJ37127; RCIX1964.
GeneIDi5144870.
KEGGirci:RCIX1964.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciUMET351160:GJT4-1146-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. "Genome of rice cluster I archaea -- the key methane producers in the rice rhizosphere."
    Erkel C., Kube M., Reinhardt R., Liesack W.
    Science 313:370-372(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiDAPF_UNCMA
AccessioniPrimary (citable) accession number: Q0W3B6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: September 5, 2006
Last modified: January 7, 2015
This is version 57 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.