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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
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 sitei78 – 781SubstrateUniRule annotation
Active sitei87 – 871Proton donor/acceptorUniRule annotation
Binding sitei166 – 1661SubstrateUniRule annotation
Sitei168 – 1681Important for catalytic activityUniRule annotation
Binding sitei200 – 2001SubstrateUniRule annotation
Sitei218 – 2181Important for catalytic activityUniRule annotation
Active sitei227 – 2271Proton 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

BioCyciMSME246196:GJ4Y-2735-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:MSMEG_2735, MSMEI_2668
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000006158 Componenti: Chromosome UP000000757 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 – 291291Diaminopimelate epimerasePRO_1000011909Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi87 ↔ 227

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi246196.MSMEG_2735.

Structurei

3D structure databases

ProteinModelPortaliA0QVY0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 893Substrate bindingUniRule annotation
Regioni218 – 2192Substrate bindingUniRule annotation
Regioni228 – 2292Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
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.

A0QVY0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIFAKGHGTE NDFVVLPDLD AALSLTPSAV AALCDRRRGL GADGVLRVTR
60 70 80 90 100
AGAARAAGVF DRLPDGVSAG DWYMDYRNAD GSIAQMCGNG VRVFAHYLRA
110 120 130 140 150
SGLESADEFV VGSLAGPRPV VLHGFDPARA TTAEVTVEMG KANQFGAGSA
160 170 180 190 200
VVGGRSFDGL AVDVGNPHLA CVGITADDLA ALDVAAPVSF DPALFPDGVN
210 220 230 240 250
VEVLTASVDG AVSMRVHERG VGETRSCGTG TVAATVAALA HDGADTGTLR
260 270 280 290
VRIPGGEVTV TVTESTSYLR GPSVLVARGE LDPHWWHAVA G
Length:291
Mass (Da):29,791
Last modified:January 9, 2007 - v1
Checksum:iBB63840A5B690C9D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK73529.1.
CP001663 Genomic DNA. Translation: AFP39136.1.
RefSeqiYP_006567431.1. NC_018289.1.
YP_887068.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK73529; ABK73529; MSMEG_2735.
AFP39136; AFP39136; MSMEI_2668.
GeneIDi4533230.
KEGGimsm:MSMEG_2735.
PATRICi18077902. VBIMycSme59918_2703.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK73529.1.
CP001663 Genomic DNA. Translation: AFP39136.1.
RefSeqiYP_006567431.1. NC_018289.1.
YP_887068.1. NC_008596.1.

3D structure databases

ProteinModelPortaliA0QVY0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_2735.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK73529; ABK73529; MSMEG_2735.
AFP39136; AFP39136; MSMEI_2668.
GeneIDi4533230.
KEGGimsm:MSMEG_2735.
PATRICi18077902. VBIMycSme59918_2703.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMSME246196:GJ4Y-2735-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. Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C., Fraser C.M.
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  2. "Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
    Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
    Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  3. "Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
    Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
    Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.

Entry informationi

Entry nameiDAPF_MYCS2
AccessioniPrimary (citable) accession number: A0QVY0
Secondary accession number(s): I7G799
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: January 9, 2007
Last modified: March 4, 2015
This is version 63 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.