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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Synechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
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 sitei15 – 151SubstrateUniRule annotation
Binding sitei49 – 491SubstrateUniRule annotation
Binding sitei68 – 681SubstrateUniRule annotation
Active sitei77 – 771Proton donor/acceptorUniRule annotation
Binding sitei165 – 1651SubstrateUniRule annotation
Sitei167 – 1671Important for catalytic activityUniRule annotation
Binding sitei201 – 2011SubstrateUniRule annotation
Sitei219 – 2191Important for catalytic activityUniRule annotation
Active sitei228 – 2281Proton 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

BioCyciSSP321332:GH1B-1371-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:CYB_1371
OrganismiSynechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Taxonomic identifieri321332 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
ProteomesiUP000001938 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 – 285285Diaminopimelate epimerasePRO_1000011975Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi77 ↔ 228

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi321332.CYB_1371.

Structurei

3D structure databases

ProteinModelPortaliQ2JLR0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni12 – 132Substrate bindingUniRule annotation
Regioni77 – 793Substrate bindingUniRule annotation
Regioni219 – 2202Substrate bindingUniRule annotation
Regioni229 – 2302Substrate 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.

Q2JLR0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTPRLSFHKY QGLGNDFILV DNRWQSQPCL SPEEAVALCN RRFGVGADGV
60 70 80 90 100
IFLLPGQEGA DFSMRLFNSD GSEAEMCGNG IRCLARFLQD LGIPGRDGAY
110 120 130 140 150
QIHTLAGRIV PQVRADGLVT VDMGIPRLLA KQIPTTLVEP DEKVIRQPLA
160 170 180 190 200
VAGREWRVTA VSMGNPHCVV FLEEEGSLEE LDLAAVGPLF EHHPAFPERT
210 220 230 240 250
NTEFVQVLSP TRLRLRVWER GAGATLACGT GACAVLVAAV LEERAESQAT
260 270 280
VELPGGNLEI RWDPSTQHVW MTGPALHVFS GTTAG
Length:285
Mass (Da):30,949
Last modified:March 6, 2006 - v1
Checksum:i73DAB469419A3471
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA. Translation: ABD02344.1.
RefSeqiWP_011432994.1. NC_007776.1.
YP_477607.1. NC_007776.1.

Genome annotation databases

EnsemblBacteriaiABD02344; ABD02344; CYB_1371.
KEGGicyb:CYB_1371.
PATRICi23805070. VBISynSp29577_1388.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA. Translation: ABD02344.1.
RefSeqiWP_011432994.1. NC_007776.1.
YP_477607.1. NC_007776.1.

3D structure databases

ProteinModelPortaliQ2JLR0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi321332.CYB_1371.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD02344; ABD02344; CYB_1371.
KEGGicyb:CYB_1371.
PATRICi23805070. VBISynSp29577_1388.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciSSP321332:GH1B-1371-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. "Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses."
    Bhaya D., Grossman A.R., Steunou A.-S., Khuri N., Cohan F.M., Hamamura N., Melendrez M.C., Bateson M.M., Ward D.M., Heidelberg J.F.
    ISME J. 1:703-713(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JA-2-3B'a(2-13).

Entry informationi

Entry nameiDAPF_SYNJB
AccessioniPrimary (citable) accession number: Q2JLR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 14, 2008
Last sequence update: March 6, 2006
Last modified: March 31, 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.