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.2010 Dec 1;66(Pt 12):1552-6.
doi: 10.1107/S1744309110039801. Epub 2010 Nov 16.

Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris

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Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris

Poulami Samai et al. Acta Crystallogr Sect F Struct Biol Cryst Commun..

Abstract

CRISPRs (clustered regularly interspaced short palindromic repeats) provide bacteria and archaea with RNA-guided acquired immunity to invasive DNAs. CRISPR-associated (Cas) proteins carry out the immune effector functions. Cas2 is a universal component of the CRISPR system. Here, a 1.35 Å resolution crystal structure of Cas2 from the bacterium Desulfovibrio vulgaris (DvuCas2) is reported. DvuCas2 is a homodimer, with each protomer consisting of an N-terminal βαββαβ ferredoxin fold (amino acids 1-78) to which is appended a C-terminal segment (amino acids 79-102) that includes a short 3(10)-helix and a fifth β-strand. The β5 strands align with the β4 strands of the opposite protomers, resulting in two five-stranded antiparallel β-sheets that form a sandwich at the dimer interface. The DvuCas2 dimer is stabilized by a distinctive network of hydrophilic cross-protomer side-chain interactions.

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Figures

Figure 1
Figure 1
Structure ofDvuCas2 and comparison to other Cas2 homologs. The fold of theDvuCas2 protomer (PDB code3oq2) is shown in (a) with cyan helices and magenta β-strands. (b)–(e) show the tertiary structures of the Cas2 homologsSso1404 (PDB code2i8e),Tth1823 (PDB code1zpw),Pfu1117 (PDB code2i0x) andSso8090 (PDB code3exc) superimposed onDvuCas2 and then offset horizontally. The N- and C-termini are labeled. (f) shows a structure-based alignment of the amino-acid sequences of the five Cas2 proteins. The secondary-structure elements ofDvuCas2 are shown above the sequence, with β-strands depicted as arrows and helices as cylinders. Gaps in the alignment are indicated by dashes. The amino-acid side chains that comprise theDvuCas2 homodimer interface (Fig. 2 ▶) are denoted by dots above the sequence. Residues that are essential for the endoribonuclease activity ofSso1404 are highlighted in yellow.
Figure 2
Figure 2
Stereoviews of theDvuCas2 dimer interface. (a) The folds of theA andB protomers are rendered in magenta and green, respectively. The N-termini are indicated. Five sulfates and a citrate located at various sites on the protein surface are shown as stick models. The two sulfate sites at the bottom of the image were refined as partially occupied by sulfate and partially by citrate; only the sulfates are shown for the sake of clarity. (b) This view highlights the hydrophilic cross-protomer side-chain interactions. The secondary-structure elements are labeled as in Fig. 1 ▶(f). Side chains of theA andB protomers that comprise the dimer interface are shown as stick models with beige and green C atoms, respectively. Ionic and hydrogen-bonding contacts of side-chain atoms at the dimer interface are indicated by dashed lines.
Figure 3
Figure 3
Disposition ofDvuCas2 residues corresponding to those implicated in the endoribonuclease activity of Cas2 homologs. The folds of theA andB protomers are rendered in magenta and green, respectively. The side chains of theA andB protomers that correspond to the putativeSso1404 phosphodiesterase active-site residues (Fig. 1 ▶f) are shown as stick models with beige and green C atoms, respectively. Two sulfate anions docked on the surface of theDvuCas2A protomer are also shown as stick models. Ionic and hydrogen-bonding interactions are indicated by dashed lines.
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