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(-) Description

Title :  STRUCTURAL BASIS FOR DNASE ACTIVITY OF A CONSERVED PROTEIN IMPLICATED IN CRISPR-MEDIATED ANTIVIRAL DEFENSE
 
Authors :  B. Wiedenheft
Date :  18 Mar 09  (Deposition) - 30 Jun 09  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  Crispr, Crispr-Associated Cas1, Metallonuclease, Dnase, Prokaryotic Immune System, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Wiedenheft, K. Zhou, M. Jinek, S. M. Coyle, W. Ma, J. A. Doudna
Structural Basis For Dnase Activity Of A Conserved Protein Implicated In Crispr-Mediated Genome Defense.
Structure V. 17 904 2009
PubMed-ID: 19523907  |  Reference-DOI: 10.1016/J.STR.2009.03.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAS1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHMGWA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA14_33350
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208963
    Strain: UCBPP-PA14

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 2 (1x): A C 
Biological Unit 3 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MN4Ligand/IonMANGANESE (II) ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:190 , HIS A:254 , ASP A:268 , HOH A:451 , HOH A:526BINDING SITE FOR RESIDUE MN A 325
2AC2SOFTWAREGLY A:87 , GLY A:216 , GLY A:218 , HOH A:542BINDING SITE FOR RESIDUE NA A 326
3AC3SOFTWAREASP A:307 , ASP A:311 , HOH A:509BINDING SITE FOR RESIDUE CA A 327
4AC4SOFTWAREGLU B:190 , HIS B:254 , ASP B:268BINDING SITE FOR RESIDUE MN B 325
5AC5SOFTWAREASP B:307 , ASP B:311 , HOH B:420BINDING SITE FOR RESIDUE CA B 326
6AC6SOFTWAREGLY B:87 , GLY B:216 , GLY B:218 , HOH B:365 , HOH B:373 , HOH B:667BINDING SITE FOR RESIDUE NA B 327
7AC7SOFTWAREHIS C:254 , ASP C:268 , HOH C:506BINDING SITE FOR RESIDUE MN C 325
8AC8SOFTWAREHIS D:254 , ASP D:268BINDING SITE FOR RESIDUE MN D 325

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr C:89 -Pro C:90
2Thr D:89 -Pro D:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GOD)

(-) 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:320
 aligned with CAS1_PSEAB | Q02ML7 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
           CAS1_PSEAB     3 DISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRAQALDFMIDTLKDVAQRSTV 322
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeee..eeeeee..eeeeeeee..eeeeee.hhh.eeeeee...eeeehhhhhhhhhh..eeeee.......eee..eee.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3god A   3 DISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAmRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAmRGDEEQDFRQACLDNLSRAQALDFmIDTLKDVAQRSTV 322
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302      |312       322
                                                                                               71-MSE                                                                                                                                                                                                              284-MSE                  309-MSE         


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with CAS1_PSEAB | Q02ML7 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:319
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312         
           CAS1_PSEAB     3 DISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRAQALDFMIDTLKDVAQRST 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeee..eeeeee..eeeeeeee..eeeeee.hhh.eeeeee...eeeehhhhhhhhhh..eeeee.......eee..eee.eeeeee......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3god B   3 DISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAmRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAmRGDEEQDFRQACLDNLSRAQALDFmIDTLKDVAQRST 321
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302      |312         
                                                                                               71-MSE                                                                                                                                                                                                              284-MSE                  309-MSE        


Chain C from PDB  Type:PROTEIN  Length:293
 aligned with CAS1_PSEAB | Q02ML7 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:309
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312         
           CAS1_PSEAB    13 LHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRAQALDFMIDTLKDVAQRST 321
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeee..eeeeee..eeeeee....----.........eeee....eeehhhhhhhhhh..eeeee......eeeee.....------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3god C  13 LHSKRANLYYLQHCRVLVNGGRVEYVTDEGR----WNIPIANTTSLLLGTGTSITQAAmRELARAGVLVGFCGGGGTPLFSANEVDVE------------TEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAmRGDEEQDFRQACLDNLSRAQALDFmIDTLKDVAQRST 321
                                    22        32        42|    |  52        62        72        82        92       | -         -|      122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302      |312         
                                                         43   48                     71-MSE                      100          113                                                                                                                                                                        284-MSE                  309-MSE        


Chain D from PDB  Type:PROTEIN  Length:299
 aligned with CAS1_PSEAB | Q02ML7 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:313
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318   
           CAS1_PSEAB     9 LKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRAQALDFMIDTLKDVAQRST 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee..eeeeee..eeeeee..ee..hhhhh......eeee...eeeehhhhhhhhhh..eeeee......eeeee....--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3god D   9 LKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAmRELARAGVLVGFCGGGGTPLFSANEVDV--------------EYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAmRGDEEQDFRQACLDNLSRAQALDFmIDTLKDVAQRST 321
                                    18        28        38        48        58        68  |     78        88        98|        -     | 118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     | 288       298       308|      318   
                                                                                         71-MSE                      99            114                                                                                                                                                                       284-MSE                  309-MSE
   Legend:   → Mismatch (orange background)
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  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 3GOD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CAS1_PSEAB | Q02ML7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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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