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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Mycobacterium sp. (strain KMS)
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 sitei44 – 441SubstrateUniRule annotation
Binding sitei78 – 781SubstrateUniRule annotation
Active sitei87 – 871Proton donor/acceptorUniRule annotation
Binding sitei166 – 1661SubstrateUniRule annotation
Sitei168 – 1681Important for catalytic activityUniRule annotation
Binding sitei202 – 2021SubstrateUniRule annotation
Sitei220 – 2201Important for catalytic activityUniRule annotation
Active sitei229 – 2291Proton 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

BioCyciMSP189918:GH4X-2222-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:Mkms_2209
OrganismiMycobacterium sp. (strain KMS)
Taxonomic identifieri189918 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
ProteomesiUP000000638 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 – 293293Diaminopimelate epimerasePRO_1000011911Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi87 ↔ 229

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliA1UEZ9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 893Substrate bindingUniRule annotation
Regioni220 – 2212Substrate bindingUniRule annotation
Regioni230 – 2312Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMRIINSD.
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.

A1UEZ9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFAKGHGTQ NDFVLLPDLD ARLALTPAVV SALCDRRRGL GADGVLRVTT
60 70 80 90 100
AKAALSAGVF ERLPEGVGAG DWYMDYRNAD GSIAQMCGNG VRVFAHYLRA
110 120 130 140 150
ADLESRDEFV VGSLAGPRPV VLHGFDLAHR SRAEVTVEMG KVNLLGSGSA
160 170 180 190 200
VVGGRRFTGL GIDVGNPHLA CVDTTLTEAE LAALDVAAPV DFDPAQFPDG
210 220 230 240 250
VNVEVLTALR DGAVSMRVHE RGVGETRSCG TGTVAAAVAA LAQEGAAVGT
260 270 280 290
LDVRIPGGVV TVSVTDTTSF LRGPSELVAT GELAGEWWQS HQR
Length:293
Mass (Da):30,530
Last modified:February 6, 2007 - v1
Checksum:i25A9C82578F1765A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000518 Genomic DNA. Translation: ABL91407.1.
RefSeqiWP_011768200.1. NC_008705.1.

Genome annotation databases

EnsemblBacteriaiABL91407; ABL91407; Mkms_2209.
KEGGimkm:Mkms_2209.
PATRICi18103347. VBIMycSp70743_2715.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000518 Genomic DNA. Translation: ABL91407.1.
RefSeqiWP_011768200.1. NC_008705.1.

3D structure databases

ProteinModelPortaliA1UEZ9.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABL91407; ABL91407; Mkms_2209.
KEGGimkm:Mkms_2209.
PATRICi18103347. VBIMycSp70743_2715.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMRIINSD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMSP189918:GH4X-2222-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: KMS.

Entry informationi

Entry nameiDAPF_MYCSK
AccessioniPrimary (citable) accession number: A1UEZ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 6, 2007
Last modified: July 22, 2015
This is version 60 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.