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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
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 sitei14 – 141SubstrateUniRule annotation
Binding sitei53 – 531SubstrateUniRule annotation
Binding sitei73 – 731SubstrateUniRule annotation
Active sitei82 – 821Proton donor/acceptorUniRule annotation
Binding sitei170 – 1701SubstrateUniRule annotation
Sitei172 – 1721Important for catalytic activityUniRule annotation
Binding sitei206 – 2061SubstrateUniRule annotation
Sitei224 – 2241Important for catalytic activityUniRule annotation
Active sitei233 – 2331Proton 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

BioCyciLMON169963:LMO2018-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:lmo2018
OrganismiListeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Taxonomic identifieri169963 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesListeriaceaeListeria
ProteomesiUP000000817 Componenti: Chromosome

Organism-specific databases

GenoListiLMO2018.

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 – 329329Diaminopimelate epimerasePRO_0000149851Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi82 ↔ 233

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi169963.lmo2018.

Structurei

3D structure databases

ProteinModelPortaliQ8Y5N9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni82 – 843Substrate bindingUniRule annotation
Regioni224 – 2252Substrate bindingUniRule annotation
Regioni234 – 2352Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.
OrthoDBiEOG6ND0M5.
PhylomeDBiQ8Y5N9.

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.

Q8Y5N9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATIHFTKVH GSQNDFFLVD EEGNQIMDWS DAKRADFAIK LCDREHSLGG
60 70 80 90 100
ADGILYVTKS SEAGPIGQMR VVNSDGSIAS MCGNGLRTVA RYLLEKHALT
110 120 130 140 150
EAKVETMKAI LDVKKATSLG FDIPTYQVEI SPVKFNAESL PMNVGVEKLF
160 170 180 190 200
NQVVPELDAE LAFSAVSVPN PHLITFVDQT VLDSDRQETL ASYLNSENPY
210 220 230 240 250
FPDGVNVSFV KRLSDDAIYV RTFERGVGFT NACGTAMSAC SLIKKMLDKD
260 270 280 290 300
TFETPLNVYN DGGRVQVTAK KDEAGDISLQ LIGNATFVST GSVSYESDTV
310 320
TELTNEATPE QAQYQELVKE VKEFLKTTE
Length:329
Mass (Da):36,071
Last modified:March 1, 2002 - v1
Checksum:i9B5992BFDAEA83CD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591981 Genomic DNA. Translation: CAD00096.1.
PIRiAB1327.
RefSeqiNP_465542.1. NC_003210.1.
WP_010989871.1. NC_003210.1.

Genome annotation databases

EnsemblBacteriaiCAD00096; CAD00096; CAD00096.
GeneIDi985823.
KEGGilmo:lmo2018.
PATRICi20313235. VBILisMon69206_2066.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591981 Genomic DNA. Translation: CAD00096.1.
PIRiAB1327.
RefSeqiNP_465542.1. NC_003210.1.
WP_010989871.1. NC_003210.1.

3D structure databases

ProteinModelPortaliQ8Y5N9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi169963.lmo2018.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAD00096; CAD00096; CAD00096.
GeneIDi985823.
KEGGilmo:lmo2018.
PATRICi20313235. VBILisMon69206_2066.

Organism-specific databases

GenoListiLMO2018.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.
OrthoDBiEOG6ND0M5.
PhylomeDBiQ8Y5N9.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciLMON169963:LMO2018-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 BAA-679 / EGD-e.

Entry informationi

Entry nameiDAPF_LISMO
AccessioniPrimary (citable) accession number: Q8Y5N9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 6, 2002
Last sequence update: March 1, 2002
Last modified: May 27, 2015
This is version 74 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.