PDBsum entry 3nkd

Immune system

PDB id

3nkd

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Contents

			Protein chains

					262 a.a. *

			Waters ×266

* Residue conservation analysis

PDB id:

3nkd

Links

Name:

Immune system

Title:

Structure of crisp-associated protein cas1 from escherichia coli str. K-12

Structure:

Crispr-associated protein cas1. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 536056. Strain: k12. Gene: ecdh1_0933. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.95Å

R-factor:

0.220

R-free:

0.259

Authors:

B.Nocek,T.Skarina,N.Beloglazova,A.Savchenko,A.Joachimiak,A.Yakunin

Key ref:

M.Babu et al. (2011). A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol, 79, 484-502. PubMed id: 21219465

Date:

18-Jun-10

Release date:

25-Aug-10

PROCHECK

	Headers

	References

Protein chains

Q46896 (CAS1_ECOLI) - CRISPR-associated endonuclease Cas1 from Escherichia coli (strain K12)

Seq: Struc:					305 a.a. 262 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.1.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Mol Microbiol 79:484-502 (2011)
PubMed id: 21219465

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.
M.Babu, N.Beloglazova, R.Flick, C.Graham, T.Skarina, B.Nocek, A.Gagarinova, O.Pogoutse, G.Brown, A.Binkowski, S.Phanse, A.Joachimiak, E.V.Koonin, A.Savchenko, A.Emili, J.Greenblatt, A.M.Edwards, A.F.Yakunin.

ABSTRACT

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22337052

B.Wiedenheft, S.H.Sternberg, and J.A.Doudna (2012).
RNA-guided genetic silencing systems in bacteria and archaea.

Nature, 482, 331-338.

21552286

K.S.Makarova, D.H.Haft, R.Barrangou, S.J.Brouns, E.Charpentier, P.Horvath, S.Moineau, F.J.Mojica, Y.I.Wolf, A.F.Yakunin, J.van der Oost, and E.V.Koonin (2011).
Evolution and classification of the CRISPR-Cas systems.

Nat Rev Microbiol, 9, 467-477.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.