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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Mycobacterium abscessus (strain ATCC 19977 / DSM 44196)
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 sitei163 – 1631SubstrateUniRule annotation
Sitei165 – 1651Important for catalytic activityUniRule annotation
Binding sitei199 – 1991SubstrateUniRule 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

BioCyciMABS36809-WGS:GSQO-3059-MONOMER.
MABS561007:GJTG-3059-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:MAB_3043c
OrganismiMycobacterium abscessus (strain ATCC 19977 / DSM 44196)
Taxonomic identifieri561007 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium abscessus
ProteomesiUP000007137 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 – 295295Diaminopimelate epimerasePRO_1000099249Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi561007.MAB_3043c.

Structurei

3D structure databases

ProteinModelPortaliB1MD00.
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.
OMAiNPHTVVA.
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.

B1MD00-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFTKGHGTQ NDFVVLPDVH IKRDLSVAAV QALCDRQRGL GADGVLRVTT
60 70 80 90 100
VGAALEGGVL AEKPAGVSSE DWFMDYRNAD GSIAEMCGNG VRVFAHYLRS
110 120 130 140 150
VGLEHRDEFV VASLAGPRPV RINSWSQLTA DVTVDMGPVK EFGAGEAIVG
160 170 180 190 200
GRRFSGLAID VGNPHLACVD AVLTTEQLRI LDVGAPVTFD EQLFPDGVNV
210 220 230 240 250
EVLTAPSAGP ANTVHMRVHE RGVGETRSCG TGTVAAAYAA LRHIGQRTGE
260 270 280 290
VVVNIPGGQV RVTVTGESSF LRGPSMLLAD GEISDEWWGG IGACG
Length:295
Mass (Da):31,029
Last modified:April 29, 2008 - v1
Checksum:iF35741A749DCDDFA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU458896 Genomic DNA. Translation: CAM63121.1.

Genome annotation databases

EnsemblBacteriaiCAM63121; CAM63121; MAB_3043c.
PATRICi17977842. VBIMycAbs55940_3094.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU458896 Genomic DNA. Translation: CAM63121.1.

3D structure databases

ProteinModelPortaliB1MD00.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi561007.MAB_3043c.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAM63121; CAM63121; MAB_3043c.
PATRICi17977842. VBIMycAbs55940_3094.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
OMAiNPHTVVA.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciMABS36809-WGS:GSQO-3059-MONOMER.
MABS561007:GJTG-3059-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. "Acquisition of foreign virulence genes by the cystic fibrosis pathogen Mycobacterium abscessus."
    Genoscope
    Ripoll F., Pasek S., Schenowitz C., Dossat C., Barbe V., Rottman M., Heym B., Herrmann J.L., Daffe M., Brosch R., Risler J.L., Gaillard J.L.
    Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19977 / DSM 44196.

Entry informationi

Entry nameiDAPF_MYCA9
AccessioniPrimary (citable) accession number: B1MD00
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: July 22, 2015
This is version 56 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.