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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Mycobacterium gilvum (strain PYR-GCK) (Mycobacterium flavescens (strain ATCC 700033 / PYR-GCK))
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 sitei163 – 1631SubstrateUniRule annotation
Sitei165 – 1651Important for catalytic activityUniRule annotation
Binding sitei199 – 1991SubstrateUniRule annotation
Sitei217 – 2171Important for catalytic activityUniRule annotation
Active sitei226 – 2261Proton 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

BioCyciMGIL350054:GHK8-4007-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:Mflv_3961
OrganismiMycobacterium gilvum (strain PYR-GCK) (Mycobacterium flavescens (strain ATCC 700033 / PYR-GCK))
Taxonomic identifieri350054 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000000232 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 – 289289Diaminopimelate epimerasePRO_1000077700Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi87 ↔ 226

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi350054.Mflv_3961.

Structurei

3D structure databases

ProteinModelPortaliA4TCN3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 893Substrate bindingUniRule annotation
Regioni217 – 2182Substrate bindingUniRule annotation
Regioni227 – 2282Substrate 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.

A4TCN3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFAKGHGTQ NDFVLLPDLN AQYSLTARAV AALCDRRRGL GADGLLRVTT
60 70 80 90 100
AGAALAAGVF DRLPEGVAED DWFMDYRNAD GSIAEMCGNG VRVFAHYLHA
110 120 130 140 150
GGLEHRSEFV VGSLAGPRPV VLHEADDTTA DVTVEMGKAV RCGTGTATVG
160 170 180 190 200
GRRFSGLAVD VGNPHLACVD EELTDAGLAS LDVASPVAFD STQFPHGVNV
210 220 230 240 250
EILTAPRDGA VAMRVHERGV GETRSCGTGT VAAAVAALDH QGARTGTLRV
260 270 280
RIPGGEVCVT VTETDSYLRG PSVLLAHGEL AEQWWAAQH
Length:289
Mass (Da):30,240
Last modified:May 15, 2007 - v1
Checksum:i048DCB9B1F08D0DD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000656 Genomic DNA. Translation: ABP46432.1.
RefSeqiWP_011894812.1. NC_009338.1.
YP_001135220.1. NC_009338.1.

Genome annotation databases

EnsemblBacteriaiABP46432; ABP46432; Mflv_3961.
KEGGimgi:Mflv_3961.
PATRICi18036123. VBIMycGil17082_4032.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000656 Genomic DNA. Translation: ABP46432.1.
RefSeqiWP_011894812.1. NC_009338.1.
YP_001135220.1. NC_009338.1.

3D structure databases

ProteinModelPortaliA4TCN3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi350054.Mflv_3961.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP46432; ABP46432; Mflv_3961.
KEGGimgi:Mflv_3961.
PATRICi18036123. VBIMycGil17082_4032.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMGIL350054:GHK8-4007-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: PYR-GCK.

Entry informationi

Entry nameiDAPF_MYCGI
AccessioniPrimary (citable) accession number: A4TCN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: May 15, 2007
Last modified: April 29, 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

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.