RegulonDB RegulonDB 11.1: Gene Form
   

cas3 gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cas3 casA sokX casB CRP LeuO CRP LeuO StpA H-NS LeuO LeuO SlyA anti-terminator terminator TSS_3043 TSS_3043 casAp casAp

Gene      
Name: cas3    Texpresso search in the literature
Synonym(s): ECK2756, EG12634, b2761, ygcB
Genome position(nucleotides): 2884553 <-- 2887219
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 44.69
External database links:  
ASAP:
 ABE-0009054
ECHOBASE:
 EB2516
ECOLIHUB:
 cas3
OU-MICROARRAY:
 b2761
STRING:
 511145.b2761
COLOMBOS: cas3


Product      
Name: CRISPR-associated endonuclease/helicase Cas3
Synonym(s): Cas3, YgcB
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 100.545
Isoelectric point: 5.423
Motif(s):
 
Type Positions Sequence Comment
11 -> 235 WGKSSKSLTKGNDIHLLIYHCLDVAAVADCWWDQSVVLQNTFCRNEMLSKQRVKAWLLFFIALHDIGKFDIRFQYKSAESWLKLNPATPSLNGPSTQMCRKFNHGAAGLYWFNQDSLSEQSLGDFFSFFDAAPHPYESWFPWVEAVTGHHGFILHSQDQDKSRWEMPASLASYAAQDKQAREEWISVLEALFLTPAGLSINDIPPDCSSLLAGFCSLADWLGSWT
20 -> 231 KGNDIHLLIYHCLDVAAVADCWWDQSVVLQNTFCRNEMLSKQRVKAWLLFFIALHDIGKFDIRFQYKSAESWLKLNPATPSLNGPSTQMCRKFNHGAAGLYWFNQDSLSEQSLGDFFSFFDAAPHPYESWFPWVEAVTGHHGFILHSQDQDKSRWEMPASLASYAAQDKQAREEWISVLEALFLTPAGLSINDIPPDCSSLLAGFCSLADWL UniProt: HD Cas3-type.
74 -> 74 H UniProt: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing..
75 -> 75 D UniProt: 10% R-loop formation..
78 -> 78 K UniProt: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing..

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.10 - defense/survival
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005840 - ribosome
molecular_function GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0004386 - helicase activity
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0004527 - exonuclease activity
GO:0016787 - hydrolase activity
GO:0008296 - 3'-5'-exodeoxyribonuclease activity
GO:0046872 - metal ion binding
GO:0003723 - RNA binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
GO:0003690 - double-stranded DNA binding
GO:0000287 - magnesium ion binding
GO:0033677 - DNA/RNA helicase activity
GO:0033592 - RNA strand annealing activity
GO:0097098 - DNA/RNA hybrid annealing activity
GO:0000014 - single-stranded DNA endodeoxyribonuclease activity
biological_process GO:0000737 - DNA catabolic process, endonucleolytic
GO:0000027 - ribosomal large subunit assembly
GO:0051607 - defense response to virus
GO:0000738 - DNA catabolic process, exonucleolytic
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
[EXP-IDA] Inferred from direct assay
Reference(s): [1] Brouns SJ., et al., 2008
[2] Howard JA., et al., 2011
[3] Ivancic-Bace I., et al., 2013
[4] Luo ML., et al., 2015
[5] Majsec K., et al., 2016
[6] Mulepati S., et al., 2014
External database links:  
ALPHAFOLD:
 P38036
ECOCYC:
 EG12634-MONOMER
ECOLIWIKI:
 b2761
INTERPRO:
 IPR014001
INTERPRO:
 IPR027417
INTERPRO:
 IPR038257
INTERPRO:
 IPR011545
INTERPRO:
 IPR006474
INTERPRO:
 IPR001650
INTERPRO:
 IPR006483
PANTHER:
 PTHR24031:SF596
PFAM:
 PF18019
PFAM:
 PF00271
PFAM:
 PF00270
PRIDE:
 P38036
PROSITE:
 PS51643
PROSITE:
 PS51192
PROSITE:
 PS51194
REFSEQ:
 NP_417241
SMART:
 SM00490
SMART:
 SM00487
UNIPROT:
 P38036


Operon      
Name: cas3         
Operon arrangement:
Transcription unit        Promoter
cas3


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


RNA cis-regulatory element    
Attenuation: Transcriptional


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_3043 2884659 reverse nd [RS-EPT-CBR] [7]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Brouns SJ., Jore MM., Lundgren M., Westra ER., Slijkhuis RJ., Snijders AP., Dickman MJ., Makarova KS., Koonin EV., van der Oost J., 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes., Science 321(5891):960-4

 [2] Howard JA., Delmas S., Ivancic-Bace I., Bolt EL., 2011, Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein., Biochem J 439(1):85-95

 [3] Ivancic-Bace I., Radovcic M., Bockor L., Howard JL., Bolt EL., 2013, Cas3 stimulates runaway replication of a ColE1 plasmid in Escherichia coli and antagonises RNaseHI., RNA Biol 10(5):770-8

 [4] Luo ML., Mullis AS., Leenay RT., Beisel CL., 2015, Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression., Nucleic Acids Res 43(1):674-81

 [5] Majsec K., Bolt EL., Ivancic-Bace I., 2016, Cas3 is a limiting factor for CRISPR-Cas immunity in Escherichia coli cells lacking H-NS., BMC Microbiol 16:28

 [6] Mulepati S., Heroux A., Bailey S., 2014, Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target., Science 345(6203):1479-84

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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