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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methanocella arvoryzae (strain DSM 22066 / NBRC 105507 / MRE50)
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: 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 sitei14SubstrateUniRule annotation1
Binding sitei49SubstrateUniRule annotation1
Binding sitei67SubstrateUniRule annotation1
Active sitei76Proton donor/acceptorUniRule annotation1
Sitei161Important for catalytic activityUniRule annotation1
Binding sitei193SubstrateUniRule annotation1
Sitei210Important for catalytic activityUniRule annotation1
Active sitei220Proton donor/acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciMARV351160:G12X7-1143-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
OrganismiMethanocella arvoryzae (strain DSM 22066 / NBRC 105507 / MRE50)
Taxonomic identifieri351160 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanomicrobiaMethanocellalesMethanocellaceaeMethanocella
Proteomesi
  • UP000000663 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119791 – 280Diaminopimelate epimeraseAdd BLAST280

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
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)DescriptionActionsGraphical viewLength
Regioni76 – 78Substrate bindingUniRule annotation3
Regioni210 – 211Substrate bindingUniRule annotation2
Regioni221 – 222Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG02255. Archaea.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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.
RefSeqiWP_012035447.1. 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.
RefSeqiWP_012035447.1. 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

eggNOGiarCOG02255. Archaea.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMARV351160:G12X7-1143-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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...

Entry informationi

Entry nameiDAPF_METAR
AccessioniPrimary (citable) accession number: Q0W3B6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: September 5, 2006
Last modified: November 2, 2016
This is version 64 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

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.