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Protein

Recombination-promoting nuclease RpnA

Gene

rpnA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

A low activity DNA endonuclease yielding 3'-hydroxyl ends, equally active on ss or dsDNA, not active on dsRNA (PubMed:28096446). Shows no sequence specificity (PubMed:28096446). Upon expression enhances RecA-independent DNA recombination 49-fold, concomitantly reducing viability by 88% and probably inducing DNA damage as measured by induction of the SOS repair response in RecA cells (PubMed:28096446). RecA-independent DNA recombination leads to replacement of recipient genes with large segments of donor DNA rather than DNA addition to the donor strain; increased expression of RpnA leads to smaller replacement segments, suggesting this protein may play a role in generating crossover events (PubMed:28096446).1 Publication

Cofactori

Mg2+1 PublicationNote: Endonuclease activity partially supported by Mn2+.1 Publication

Enzyme regulationi

Inhibited by EDTA, Zn2+ and by Mg2+ plus Mn2+; stimulated by Ca2+ in the presence of Mg2+.1 Publication

pH dependencei

Optimum pH is 9.0, active between pH 7.5 and 10.5.1 Publication

GO - Molecular functioni

  • endodeoxyribonuclease activity, producing 5'-phosphomonoesters Source: UniProtKB

GO - Biological processi

  • DNA recombination Source: UniProtKB

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease
Biological processDNA recombination
LigandMagnesium

Enzyme and pathway databases

BioCyciEcoCyc:EG11750-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Recombination-promoting nuclease RpnA1 Publication (EC:3.1.21.-1 Publication)
Gene namesi
Name:rpnA1 Publication
Synonyms:yhgA
Ordered Locus Names:b3411, JW3374
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11750. yhgA.

Pathology & Biotechi

Disruption phenotypei

Cells grow to slightly higher density than wild-type in sublethal levels of streptomycin (PubMed:25316676). A quadruple rpnA-rpnB-rpnC-rpnD deletion shows no change in basal RecA-independent recombination (PubMed:28096446).2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi11D → A: No longer increases recombination efficiency, toxicity or SOS response. 1 Publication1
Mutagenesisi63D → A: No longer increases recombination efficiency, toxicity or SOS response. No nuclease activity. 1 Publication1
Mutagenesisi82E → A: No longer increases recombination efficiency, toxicity or SOS response. 1 Publication1
Mutagenesisi84Q → A: No longer increases recombination efficiency or SOS response, more toxic than wild-type. 1 Publication1
Mutagenesisi84Q → K: No longer increases recombination efficiency, toxicity or SOS response. 1 Publication1
Mutagenesisi94R → A: No longer increases recombination efficiency or SOS response, more toxic than wild-type. 1 Publication1
Mutagenesisi165D → A: Hyperactive mutant, increases recombination efficiency, more toxic than wild-type. Increased nuclease activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001695441 – 292Recombination-promoting nuclease RpnAAdd BLAST292

Proteomic databases

PaxDbiP31667.
PRIDEiP31667.

Interactioni

Protein-protein interaction databases

BioGridi4263493. 9 interactors.
DIPiDIP-12335N.
IntActiP31667. 1 interactor.
MINTiMINT-1248711.
STRINGi316407.85676630.

Structurei

3D structure databases

ProteinModelPortaliP31667.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the Rpn/YhgA-like nuclease family.Curated

Phylogenomic databases

eggNOGiENOG4105DNE. Bacteria.
COG5464. LUCA.
HOGENOMiHOG000116866.
InParanoidiP31667.
PhylomeDBiP31667.

Family and domain databases

InterProiView protein in InterPro
IPR010106. RpnA.
IPR006842. Transposase_31.
PfamiView protein in Pfam
PF04754. Transposase_31. 1 hit.
TIGRFAMsiTIGR01784. T_den_put_tspse. 1 hit.

Sequencei

Sequence statusi: Complete.

P31667-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKKQSSTPH DALFKLFLRQ PDTARDFLAF HLPAPIHALC DMKTLKLESS
60 70 80 90 100
SFIDDDLRES YSDVLWSVKT EQGPGYIYCL IEHQSTSNKL IAFRMMRYAI
110 120 130 140 150
AAMQNHLDAG YKTLPMVVPL LFYHGIESPY PYSLCWLDCF ADPKLARQLY
160 170 180 190 200
ASAFPLIDVT VMPDDEIMQH RRMALLELIQ KHIRQRDLMG LVEQMACLLS
210 220 230 240 250
SGYANDRQIK GLFNYILQTG DAVRFNDFID GVAERSPKHK ESLMTIAERL
260 270 280 290
RQEGEQSKAL HIAKIMLESG VPLADIMRFT GLSEEELAAA SQ
Length:292
Mass (Da):33,267
Last modified:July 1, 1993 - v1
Checksum:iFF3DF73DBBAF087E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15587 Genomic DNA. No translation available.
U18997 Genomic DNA. Translation: AAA58209.1.
U00096 Genomic DNA. Translation: AAC76436.1.
AP009048 Genomic DNA. Translation: BAE77880.1.
PIRiF65136.
RefSeqiNP_417870.1. NC_000913.3.
WP_000039062.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76436; AAC76436; b3411.
BAE77880; BAE77880; BAE77880.
GeneIDi947917.
KEGGiecj:JW3374.
eco:b3411.
PATRICifig|1411691.4.peg.3318.

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 one 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.

Entry informationi

Entry nameiRPNA_ECOLI
AccessioniPrimary (citable) accession number: P31667
Secondary accession number(s): Q2M776
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: July 5, 2017
This is version 116 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families