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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei53 – 531SubstrateUniRule annotation
Binding sitei73 – 731SubstrateUniRule annotation
Active sitei82 – 821Proton donor/acceptorUniRule annotation
Binding sitei172 – 1721SubstrateUniRule annotation
Sitei174 – 1741Important for catalytic activityUniRule annotation
Binding sitei209 – 2091SubstrateUniRule annotation
Sitei227 – 2271Important for catalytic activityUniRule annotation
Active sitei236 – 2361Proton 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

BioCyciLPLA220668-WGS:GSPK-1867-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:lp_2185
OrganismiLactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Taxonomic identifieri220668 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
ProteomesiUP000000432 Componenti: Chromosome

Subcellular locationi

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 – 332332Diaminopimelate epimerasePRO_0000149845Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi82 ↔ 236

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi220668.lp_2185.

Structurei

3D structure databases

ProteinModelPortaliQ88V90.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni82 – 843Substrate bindingUniRule annotation
Regioni227 – 2282Substrate bindingUniRule annotation
Regioni237 – 2382Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.

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.

Q88V90-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVKMIKVHG SGNDFYLLDQ TQFQAPLSDA DLKQLAINIC KRDGAGLYDG
60 70 80 90 100
ADGVLVVDKS EHPQVLGRMR VINADGTEAS MCGNGLRTVA RYLGTQNSQE
110 120 130 140 150
DFRVQTMYAD LKVQAVADFA AHVPAYSVEI SPVTFDAQTL GMHANNDATT
160 170 180 190 200
IINEKIPALS ADLKFSAVAV PNPHLIAFVD HDTLVGPELG RIGEWMNDGK
210 220 230 240 250
NQIFPDGVNV SFVEVLGPNS IFVRTFERGV GFTNACGTAM SASSLMYVLL
260 270 280 290 300
HQESTDFNQE IHVTNPGGMV KTVVHQGADE EYWMELIGNA TFVRIVTLPL
310 320 330
EDALQGDYSP VTATETGEQV AYEDFVANLA KA
Length:332
Mass (Da):35,962
Last modified:June 20, 2003 - v1
Checksum:i1D5FF6C6E05441E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL935263 Genomic DNA. Translation: CCC79406.1.
RefSeqiYP_004889920.1. NC_004567.2.

Genome annotation databases

EnsemblBacteriaiCCC79406; CCC79406; lp_2185.
GeneIDi1063577.
KEGGilpl:lp_2185.
PATRICi22250413. VBILacPla27411_1847.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL935263 Genomic DNA. Translation: CCC79406.1.
RefSeqiYP_004889920.1. NC_004567.2.

3D structure databases

ProteinModelPortaliQ88V90.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi220668.lp_2185.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCC79406; CCC79406; lp_2185.
GeneIDi1063577.
KEGGilpl:lp_2185.
PATRICi22250413. VBILacPla27411_1847.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiWMELIGN.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciLPLA220668-WGS:GSPK-1867-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-793 / NCIMB 8826 / WCFS1.

Entry informationi

Entry nameiDAPF_LACPL
AccessioniPrimary (citable) accession number: Q88V90
Secondary accession number(s): F9UQB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2003
Last sequence update: June 20, 2003
Last modified: January 7, 2015
This is version 70 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.