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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
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

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 sitei12 – 121SubstrateUniRule annotation
Binding sitei48 – 481SubstrateUniRule annotation
Binding sitei67 – 671SubstrateUniRule annotation
Active sitei76 – 761Proton donor/acceptorUniRule annotation
Binding sitei165 – 1651SubstrateUniRule annotation
Sitei167 – 1671Important for catalytic activityUniRule annotation
Binding sitei198 – 1981SubstrateUniRule annotation
Sitei216 – 2161Important for catalytic activityUniRule annotation
Active sitei225 – 2251Proton 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

BioCyciMTHE187420:GJNM-1336-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:MTH_1334
OrganismiMethanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
Taxonomic identifieri187420 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanothermobacter
ProteomesiUP000005223 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 – 286286Diaminopimelate epimerasePRO_0000149888Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 225

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi187420.MTH1334.

Structurei

3D structure databases

ProteinModelPortaliO27389.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 102Substrate bindingUniRule annotation
Regioni76 – 783Substrate bindingUniRule annotation
Regioni216 – 2172Substrate bindingUniRule annotation
Regioni226 – 2272Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMRIINSD.

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.

O27389-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILFSKMHGL GNDYVVIDES AQECIPEDKK PEFVREVCTR GFSVGADGVI
60 70 80 90 100
FVQPASGEGD IRFRIFNADG SEAEMCGNGI RCFSKFVYDN AIVRKRRLEV
110 120 130 140 150
ETLAGIKTVE LEVEDGAVVS SRVDMGTATF KTDQIPMDVE EYEFIDRFLP
160 170 180 190 200
VEGEDIKLTA LSVGNPHAII FVDDAEGVDL DRLGPAIENH PLFPERINVH
210 220 230 240 250
FVEVVSPSEI IMVTWERGAG PTMACGTGAT ASVIAGVKLE KLDDSVLVHL
260 270 280
PGGELKIDVY QDGTELGAYM EGDAVMVFDG ILLRDP
Length:286
Mass (Da):31,220
Last modified:May 30, 2000 - v2
Checksum:i374300C9D7FBDDE7
GO

Sequence cautioni

The sequence AAB85812.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000666 Genomic DNA. Translation: AAB85812.1. Different initiation.
PIRiD69044.
RefSeqiNP_276451.1. NC_000916.1.
WP_010876947.1. NC_000916.1.

Genome annotation databases

EnsemblBacteriaiAAB85812; AAB85812; MTH_1334.
GeneIDi1471051.
KEGGimth:MTH1334.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000666 Genomic DNA. Translation: AAB85812.1. Different initiation.
PIRiD69044.
RefSeqiNP_276451.1. NC_000916.1.
WP_010876947.1. NC_000916.1.

3D structure databases

ProteinModelPortaliO27389.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi187420.MTH1334.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB85812; AAB85812; MTH_1334.
GeneIDi1471051.
KEGGimth:MTH1334.

Phylogenomic databases

eggNOGiCOG0253.
KOiK01778.
OMAiMRIINSD.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMTHE187420:GJNM-1336-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 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H.

Entry informationi

Entry nameiDAPF_METTH
AccessioniPrimary (citable) accession number: O27389
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 30, 2000
Last modified: July 22, 2015
This is version 94 of the entry and version 2 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.