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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Ruminiclostridium thermocellum)
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 sitei44 – 441SubstrateUniRule annotation
Binding sitei62 – 621SubstrateUniRule annotation
Active sitei71 – 711Proton donor/acceptorUniRule annotation
Binding sitei160 – 1601SubstrateUniRule annotation
Sitei162 – 1621Important for catalytic activityUniRule annotation
Binding sitei193 – 1931SubstrateUniRule annotation
Sitei211 – 2111Important 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

BioCyciCTHE203119:GIW8-3218-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:Cthe_3100
OrganismiClostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Ruminiclostridium thermocellum)
Taxonomic identifieri203119 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesRuminococcaceaeRuminiclostridium
ProteomesiUP000002145 Componenti: Chromosome

Subcellular locationi

  1. 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_1000124407Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi71 ↔ 220

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi203119.Cthe_3100.

Structurei

3D structure databases

ProteinModelPortaliA3DK16.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate bindingUniRule annotation
Regioni71 – 733Substrate bindingUniRule annotation
Regioni211 – 2122Substrate bindingUniRule annotation
Regioni221 – 2222Substrate 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.

A3DK16-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFTKMHGLG NDYIYVNCFE ETVENPSEVA KKVSDRHFGI GSDGLVLIMP
60 70 80 90 100
SERADFKMRM FNSDGSEAEM CGNAIRCVGK YVFDRGMTNK NVIRVETLAG
110 120 130 140 150
IKVLELTVQD GKAKLVKVDM GEPILKPENI PVNSDKEIFR TEPVEIDGKE
160 170 180 190 200
FKVTCVSMGN PHAVSYVKNV DIFPLEKIGP KMEHHPLFPK RINAEFVEVI
210 220 230 240 250
DRTTLKMRVW ERGAGETLAC GTGACAVLVA SVLNGVSERK ATVKLLGGDL
260 270 280
IIEWNENNNH VYMTGPAVKV FEGEVDLNEL
Length:280
Mass (Da):31,124
Last modified:March 20, 2007 - v1
Checksum:iCE9C58BBF38D6A3C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000568 Genomic DNA. Translation: ABN54295.1.
RefSeqiYP_001039488.1. NC_009012.1.

Genome annotation databases

EnsemblBacteriaiABN54295; ABN54295; Cthe_3100.
KEGGicth:Cthe_3100.
PATRICi19520340. VBICloThe47081_3312.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000568 Genomic DNA. Translation: ABN54295.1.
RefSeqiYP_001039488.1. NC_009012.1.

3D structure databases

ProteinModelPortaliA3DK16.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi203119.Cthe_3100.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABN54295; ABN54295; Cthe_3100.
KEGGicth:Cthe_3100.
PATRICi19520340. VBICloThe47081_3312.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCTHE203119:GIW8-3218-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 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372.

Entry informationi

Entry nameiDAPF_CLOTH
AccessioniPrimary (citable) accession number: A3DK16
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 20, 2007
Last modified: April 1, 2015
This is version 62 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.