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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Nitratiruptor sp. (strain SB155-2)
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

Pathway:iL-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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111SubstrateUniRule annotation
Binding sitei42 – 421SubstrateUniRule annotation
Binding sitei60 – 601SubstrateUniRule annotation
Active sitei69 – 691Proton donor/acceptorUniRule annotation
Sitei138 – 1381Important for catalytic activityUniRule annotation
Binding sitei164 – 1641SubstrateUniRule annotation
Sitei182 – 1821Important for catalytic activityUniRule annotation
Active sitei192 – 1921Proton donor/acceptorUniRule annotation

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

BioCyciNSP387092:GHA5-102-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:NIS_0102
OrganismiNitratiruptor sp. (strain SB155-2)
Taxonomic identifieri387092 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaNitratiruptor
ProteomesiUP000001118 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 250250Diaminopimelate epimerasePRO_1000011920Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi69 ↔ 192

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi387092.NIS_0102.

Structurei

3D structure databases

ProteinModelPortaliA6Q160.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni69 – 713Substrate bindingUniRule annotation
Regioni182 – 1832Substrate bindingUniRule annotation
Regioni193 – 1942Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLAKQVCH.
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.

A6Q160-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQLVKYSASG NDFVIYHTFV KKDRSELAKL LCHRHEGIGA DGLIVLLPHS
60 70 80 90 100
RYDFEWQFYN ADGSEAEMCG NGSRAAAHYA YSYGLASKQM RFLTLAGVIE
110 120 130 140 150
ASVEADVVES QLTKPKILDR KIEENGKRWW LIDTGVPHLV TFVEDLNQFD
160 170 180 190 200
KNESKRLRNK YNANVNYGII RDLENVGVRT YERGVEDETL ACGTGMAATF
210 220 230 240 250
LRAFEEGVVN PTVTVVPKSG EELQLRYENE KLFFKGRVKK VFETFKEGIW
Length:250
Mass (Da):28,476
Last modified:August 21, 2007 - v1
Checksum:iA9EDE4FAA3305FEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009178 Genomic DNA. Translation: BAF69219.1.
RefSeqiWP_011979645.1. NC_009662.1.

Genome annotation databases

EnsemblBacteriaiBAF69219; BAF69219; NIS_0102.
KEGGinis:NIS_0102.
PATRICi22682136. VBINitSp82229_0109.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009178 Genomic DNA. Translation: BAF69219.1.
RefSeqiWP_011979645.1. NC_009662.1.

3D structure databases

ProteinModelPortaliA6Q160.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi387092.NIS_0102.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF69219; BAF69219; NIS_0102.
KEGGinis:NIS_0102.
PATRICi22682136. VBINitSp82229_0109.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLAKQVCH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciNSP387092:GHA5-102-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. "Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens."
    Nakagawa S., Takaki Y., Shimamura S., Reysenbach A.-L., Takai K., Horikoshi K.
    Proc. Natl. Acad. Sci. U.S.A. 104:12146-12150(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SB155-2.

Entry informationi

Entry nameiDAPF_NITSB
AccessioniPrimary (citable) accession number: A6Q160
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 21, 2007
Last modified: July 22, 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.