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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
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: 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei6 – 61SubstrateUniRule annotation
Binding sitei39 – 391SubstrateUniRule annotation
Binding sitei57 – 571SubstrateUniRule annotation
Active sitei66 – 661Proton donor/acceptorUniRule annotation
Sitei138 – 1381Important for catalytic activityUniRule annotation
Binding sitei170 – 1701SubstrateUniRule annotation
Sitei188 – 1881Important for catalytic activityUniRule annotation
Active sitei198 – 1981Proton 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

BioCyciCTEP194439:GHN0-2061-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:CT2021
OrganismiChlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
Taxonomic identifieri194439 [NCBI]
Taxonomic lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeChlorobaculum
ProteomesiUP000001007 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 – 257257Diaminopimelate epimerasePRO_0000149832Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi66 ↔ 198

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi194439.CT2021.

Structurei

3D structure databases

ProteinModelPortaliQ8KAX9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni66 – 683Substrate bindingUniRule annotation
Regioni188 – 1892Substrate bindingUniRule annotation
Regioni199 – 2002Substrate 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.

Q8KAX9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGAGNDFIV IDNRQGLFNL THEQVRAMCT RRTGIGADGL ILLETSETAD
60 70 80 90 100
FRMNYHNADG FPGTMCGNGG RCAVWFAHLI GIRPTGKHYR FEAGPSTYEA
110 120 130 140 150
EVTGEESVRL HMLPPSDFRD GLQAGAWNCH FVDTGSPHAI AYVNNLDQLD
160 170 180 190 200
VLTEGGNIRH NKELFPDGTN VNFLEITAPD ALSIRTFERG VEDETLACGT
210 220 230 240 250
GTVAAALMSF RLGKVTSSLV RVKVKSGETL MVGFNEMMDE IYLEGPARAV

YRGTITL
Length:257
Mass (Da):28,053
Last modified:October 1, 2002 - v1
Checksum:iA25BD74CE3A5E9A5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006470 Genomic DNA. Translation: AAM73238.1.
RefSeqiNP_662896.1. NC_002932.3.
WP_010933676.1. NC_002932.3.

Genome annotation databases

EnsemblBacteriaiAAM73238; AAM73238; CT2021.
GeneIDi1007540.
KEGGicte:CT2021.
PATRICi21401855. VBIChlTep116050_1831.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006470 Genomic DNA. Translation: AAM73238.1.
RefSeqiNP_662896.1. NC_002932.3.
WP_010933676.1. NC_002932.3.

3D structure databases

ProteinModelPortaliQ8KAX9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi194439.CT2021.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM73238; AAM73238; CT2021.
GeneIDi1007540.
KEGGicte:CT2021.
PATRICi21401855. VBIChlTep116050_1831.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCTEP194439:GHN0-2061-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 49652 / DSM 12025 / NBRC 103806 / TLS.

Entry informationi

Entry nameiDAPF_CHLTE
AccessioniPrimary (citable) accession number: Q8KAX9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 11, 2003
Last sequence update: October 1, 2002
Last modified: May 27, 2015
This is version 77 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.