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(-) Description

Title :  CRYSTAL STRUCTURE OF CAS6 WITH ITS SUBSTRATE RNA
 
Authors :  R. Wang, G. Preamplume, H. Li
Date :  11 Nov 10  (Deposition) - 09 Mar 11  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,G,R,X
Biol. Unit 1:  A,G  (1x)
Biol. Unit 2:  R,X  (1x)
Keywords :  Cas6, Crispr, Endonuclease, Ferridoxin Fold, Crispr Processing Endonuclease, Repeat Rna, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wang, G. Preamplume, M. P. Terns, R. M. Terns, H. Li
Interaction Of The Cas6 Riboendonuclease With Crispr Rnas: Recognition And Cleavage.
Structure V. 19 257 2011
PubMed-ID: 21300293  |  Reference-DOI: 10.1016/J.STR.2010.11.014

(-) Compounds

Molecule 1 - CAS6 PROTEIN
    Chains: A, X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PF1131
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: CRISPR PROCESSING ENZYME
 
Molecule 2 - 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'
    Chains: G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'
    Chains: R
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : AGRX
Biological Unit 1 (1x): AG  
Biological Unit 2 (1x):   RX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3PKM)

(-) Sites  (0, 0)

(no "Site" information available for 3PKM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PKM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:2 -His A:3
2Pro A:108 -Glu A:109
3Lys A:201 -Pro A:202
4Pro X:108 -Glu X:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PKM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PKM)

(-) Exons   (0, 0)

(no "Exon" information available for 3PKM)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:229
 aligned with CAS6_PYRFU | Q8U1S4 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:244
                                 1                                                                                                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    
           CAS6_PYRFU     - -----MRFLIRLVPEDKDRAFKVPYNHQYYLQGLIYNAIKSSNPKLATYLHEVKGPKLFTYSLFMAEKREHPKGLPYFLGYKKGFFYFSTCVPEIAEALVNGLLMNPEVRLWDERFYLHEIKVLREPKKFNGSTFVTLSPIAVTVVRKGKSYDVPPMEKEFYSIIKDDLQDKYVMAYGDKPPSEFEMEVLIAKPKRFRIKPGIYQTAWHLVFRAYGNDDLLKVGYEVGFGEKNSLGFGMVKVEG 239
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.------..........hhhhhhhhhhhh.hhhhhhhhhhh.....eee...........----.......eeeeeee.hhhhhhhhhhhhhh............eeeeee..........eeee.........-----........hhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeeeee...eeeeeeeeeeeeeehhhhhhhhhhh............eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pkm A   2 HHHHGSRFLIRLV------AFKVPYNHQYYLQGLIYNAIKSSNPKLATYLHEVKGPKLFTYSLFMAEKREHP----YFLGYKKGFFYFSTCVPEIAEALVNGLLMNPEVRLWDERFYLHEIKVLREPKKFNGSTFVTLSPIAVTVV-----YDVPPMEKEFYSIIKDDLQDKYVMAYGDKPPSEFEMEVLIAKPKRFRIKPGIYQTAWHLVFRAYGNDDLLKVGYEVGFGEKNSLGFGMVKVEG 245
                                    11  |     21        31        41        51        61        71 |    | 81        91       101       111       121       131       141     |   - |     161       171       181       191       201       211       221       231       241    
                                       14     21                                                  73   78                                                                  147   153                                                                                            


Chain G from PDB  Type:RNA  Length:9
                                         
                 3pkm G   2 UUACAAUAA  10


Chain R from PDB  Type:RNA  Length:9
                                         
                 3pkm R   2 UUACAAUAA  10


Chain X from PDB  Type:PROTEIN  Length:233
 aligned with CAS6_PYRFU | Q8U1S4 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:244
                                 1                                                                                                                                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    
           CAS6_PYRFU     - -----MRFLIRLVPEDKDRAFKVPYNHQYYLQGLIYNAIKSSNPKLATYLHEVKGPKLFTYSLFMAEKREHPKGLPYFLGYKKGFFYFSTCVPEIAEALVNGLLMNPEVRLWDERFYLHEIKVLREPKKFNGSTFVTLSPIAVTVVRKGKSYDVPPMEKEFYSIIKDDLQDKYVMAYGDKPPSEFEMEVLIAKPKRFRIKPGIYQTAWHLVFRAYGNDDLLKVGYEVGFGEKNSLGFGMVKVEG 239
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhheeeeeee.-------.ee..hhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eee...........----.ee....eeeeeee.hhhhhhhhhhhhhh....ee..ee..eeeeee..........eeee......................hhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeeee.....eeeeeeeeeeeeehhhhhhhhhhh............eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pkm X   2 HHHHGSRFLIRLV-------FKVPYNHQYYLQGLIYNAIKSSNPKLATYLHEVKGPKLFTYSLFMAEKREHP----YFLGYKKGFFYFSTCVPEIAEALVNGLLMNPEVRLWDERFYLHEIKVLREPKKFNGSTFVTLSPIAVTVVRKGKSYDVPPMEKEFYSIIKDDLQDKYVMAYGDKPPSEFEMEVLIAKPKRFRIKPGIYQTAWHLVFRAYGNDDLLKVGYEVGFGEKNSLGFGMVKVEG 245
                                    11  |      -|       31        41        51        61        71 |    | 81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
                                       14      22                                                 73   78
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3PKM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PKM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PKM)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,X   (CAS6_PYRFU | Q8U1S4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0043571    maintenance of CRISPR repeat elements    Any process involved in sustaining CRISPR repeat clusters, including capture of new spacer elements, expansion or contraction of clusters, propagation of the leader sequence and repeat clusters within a genome, transfer of repeat clusters and CRISPR-associated (cas) genes to new genomes, transcription of the CRISPR repeat arrays into RNA and processing, and interaction of CRISPR/cas loci with the host genome. CRISPR (clustered regularly interspaced short palindromic repeat) elements are a family of sequence elements containing multiple direct repeats of 24-48 bp with weak dyad symmetry which are separated by regularly sized nonrepetitive spacer sequences.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  Cis Peptide Bonds
    His A:2 - His A:3   [ RasMol ]  
    Lys A:201 - Pro A:202   [ RasMol ]  
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 Related Entries

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        CAS6_PYRFU | Q8U1S4: 3i4h

(-) Related Entries Specified in the PDB File

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