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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYO-EM STRUCTURE OF ACTIVATED AND OLIGOMERIC RESTRICTION ENDONUCLEASE SGRAI
 
Authors :  D. Lyumkis, H. Talley, A. Stewart, S. Shah, C. K. Park, F. Tama, C. S. Pott B. Carragher, N. C. Horton
Date :  23 Aug 13  (Deposition) - 11 Sep 13  (Release) - 30 Oct 13  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  8.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hydrolase, Restriction Endonuclease, Allostery, Dna Cleavage, Parasite-Host Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lyumkis, H. Talley, A. Stewart, S. Shah, C. K. Park, F. Tama, C. S. Potter, B. Carragher, N. C. Horton
Allosteric Regulation Of Dna Cleavage And Sequence- Specificity Through Run-On Oligomerization.
Structure V. 21 1848 2013
PubMed-ID: 24055317  |  Reference-DOI: 10.1016/J.STR.2013.08.012

(-) Compounds

Molecule 1 - SGRAIR RESTRICTION ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A_SGRA1R
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN, RESIDUES 2-338
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
    Other Details: AN SGRAI DIMER. THE OLIGOMERIC HELIX IS FORMED FROM MULTIPLE COPIES OF SUCH SGRAI DIMERS BOUND TO DNA.
    Synonym: SGRAI
 
Molecule 2 - 5'-D(*GP*AP*TP*GP*CP*GP*TP*GP*GP*GP*TP*CP*TP*TP *CP*AP*CP*AP)-3'
    Chains: C, D
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
    Other Details: 2 COPIES OF PRE-CLEAVED DNA CONTAINING STICKY ENDS AND THE SGRAI RECOGNITION SEQUENCE
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*CP*GP*GP*TP*GP*TP*GP*AP*AP*GP*AP*CP*CP *CP*AP*CP*GP*CP*AP*TP*CP)-3'
    Chains: E, F
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
    Other Details: 2 COPIES OF PRE-CLEAVED DNA CONTAINING STICKY ENDS AND THE SGRAI RECOGNITION SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4C3G)

(-) Sites  (0, 0)

(no "Site" information available for 4C3G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C3G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C3G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C3G)

(-) Exons   (0, 0)

(no "Exon" information available for 4C3G)

(-) Sequences/Alignments

Asymmetric/Biological 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:333
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVN 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................................................................................................................................................................................----................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c3g A   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAE----VHRAIRELYVPPTAADLARRFFAFLNERMELVN 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    |  311       321       331       
                                                                                                                                                                                                                                                                                                                                     301  306                                


Chain B from PDB  Type:PROTEIN  Length:333
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVN 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................................................................................................................................................................................----................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c3g B   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAE----VHRAIRELYVPPTAADLARRFFAFLNERMELVN 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    |  311       321       331       
                                                                                                                                                                                                                                                                                                                                     301  306                                


Chain C from PDB  Type:DNA  Length:18
                                                  
                 4c3g C   1 GATGCGTGGGTCTTCACA  18
                                    10        


Chain D from PDB  Type:DNA  Length:18
                                                  
                 4c3g D   1 GATGCGTGGGTCTTCACA  18
                                    10        


Chain E from PDB  Type:DNA  Length:22
                                                      
                 4c3g E  19 CCGGTGTGAAGACCCACGCATC  40
                                    28        38  


Chain F from PDB  Type:DNA  Length:22
                                                      
                 4c3g F  19 CCGGTGTGAAGACCCACGCATC  40
                                    28        38
   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 4C3G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C3G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C3G)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9F6L0_STRGR | Q9F6L0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.

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        Q9F6L0_STRGR | Q9F6L0: 3dpg 3dvo 3dw9 3mq6 3mqy 3n78 3n7b

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