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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Natranaerobius thermophilus (strain ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF)
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 sitei11 – 111SubstrateUniRule annotation
Binding sitei41 – 411SubstrateUniRule annotation
Binding sitei63 – 631SubstrateUniRule annotation
Active sitei72 – 721Proton donor/acceptorUniRule annotation
Sitei179 – 1791Important for catalytic activityUniRule annotation
Binding sitei211 – 2111SubstrateUniRule annotation
Sitei229 – 2291Important for catalytic activityUniRule annotation
Active sitei238 – 2381Proton 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

BioCyciNTHE457570:GHRL-1962-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:Nther_1913
OrganismiNatranaerobius thermophilus (strain ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF)
Taxonomic identifieri457570 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaNatranaerobialesNatranaerobiaceaeNatranaerobius
ProteomesiUP000001683: 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 – 299299Diaminopimelate epimerasePRO_1000099251Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi72 ↔ 238

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi457570.Nther_1913.

Structurei

3D structure databases

ProteinModelPortaliB2A663.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate bindingUniRule annotation
Regioni72 – 743Substrate bindingUniRule annotation
Regioni229 – 2302Substrate bindingUniRule annotation
Regioni239 – 2402Substrate 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.

B2A663-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFEKMHGLG NDFILMKDFQ RNYPDLAKRL CDRRFGIGAD GLVIYSSCKN
60 70 80 90 100
SNINADYQMR IYNSDGSEAE MCGNAIRCLA KYLAKTEETD GKRLAIATTA
110 120 130 140 150
GIKRVEIVEN FDLMGEINLS GMVGSQEQLV KVNMEKPLLK SSDIPLAVKN
160 170 180 190 200
DRNDIARQRP IDTPYGIYYL TEVSTGPPHA VIFVQNLLPE EQLLELGPII
210 220 230 240 250
EKHDLFPYGT NVEFVKVESS NHLRVQVWER GAGKTLACGT GACAVVVAAT
260 270 280 290
INGFCNGMAY VELPGGKLFI NWDNNTEELY MIGPAEHVYS GELNNQIFY
Length:299
Mass (Da):33,320
Last modified:May 20, 2008 - v1
Checksum:i181CEAF185CCD93A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001034 Genomic DNA. Translation: ACB85484.1.
RefSeqiYP_001918072.1. NC_010718.1.

Genome annotation databases

EnsemblBacteriaiACB85484; ACB85484; Nther_1913.
GeneIDi6315293.
KEGGinth:Nther_1913.
PATRICi22672546. VBINatThe92436_1962.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001034 Genomic DNA. Translation: ACB85484.1.
RefSeqiYP_001918072.1. NC_010718.1.

3D structure databases

ProteinModelPortaliB2A663.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi457570.Nther_1913.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB85484; ACB85484; Nther_1913.
GeneIDi6315293.
KEGGinth:Nther_1913.
PATRICi22672546. VBINatThe92436_1962.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciNTHE457570:GHRL-1962-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. "Complete sequence of chromosome of Natranaerobius thermophilus JW/NM-WN-LF."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.
    , Kyrpides N., Lykidis A., Mesbah N.M., Wiegel J.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF.

Entry informationi

Entry nameiDAPF_NATTJ
AccessioniPrimary (citable) accession number: B2A663
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: March 4, 2015
This is version 47 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.