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(-) Description

Title :  SGRAI WITH CLEAVED DNA AND MAGNESIUM BOUND
 
Authors :  P. W. Dunten, N. C. Horton, E. J. Little
Date :  28 Apr 10  (Deposition) - 24 Nov 10  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Restriction Enzyme-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Little, P. W. Dunten, J. Bitinaite, N. C. Horton
New Clues In The Allosteric Activation Of Dna Cleavage By Sgrai: Structures Of Sgrai Bound To Cleaved Primary-Site Dn And Uncleaved Secondary-Site Dna.
Acta Crystallogr. , Sect. D V. 67 67 2011
PubMed-ID: 21206063  |  Reference-DOI: 10.1107/S0907444910047785

(-) Compounds

Molecule 1 - SGRAIR RESTRICTION ENZYME
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A_SGRAIR
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SGRAIR
    Mutation: YES
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
 
Molecule 2 - DNA (5'-D(*GP*AP*GP*TP*CP*CP*A)-3')
    Chains: C, E
    Engineered: YES
    Fragment: CLEAVED PRIMARY SITE DNA, 5-PRIME FRAGMENT
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*CP*GP*GP*TP*GP*GP*AP*CP*TP*C)-3')
    Chains: D, F
    Engineered: YES
    Fragment: CLEAVED PRIMARY SITE DNA, 3-PRIME FRAGMENT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:188 , PHE A:241 , HOH A:340 , HOH A:341 , HOH A:342 , DC F:8BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWAREGLU A:103 , ASN A:149 , LEU A:150 , ASP A:188 , HOH A:393BINDING SITE FOR RESIDUE MG A 501
3AC3SOFTWAREHOH B:1 , ASP B:188 , PHE B:241 , HOH B:340 , HOH B:341 , DC D:8BINDING SITE FOR RESIDUE MG B 500
4AC4SOFTWAREGLU B:103 , ASN B:149 , LEU B:150 , ASP B:188 , HOH B:353 , HOH B:454BINDING SITE FOR RESIDUE MG B 501
5AC5SOFTWAREASP B:188 , HOH B:353 , HOH B:455 , HOH B:464 , HOH B:465 , DC D:8BINDING SITE FOR RESIDUE MG D 502
6AC6SOFTWAREASP A:188 , HOH A:394 , HOH A:395 , HOH A:396 , HOH A:397 , DC F:8BINDING SITE FOR RESIDUE MG F 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:129 -Pro A:130
2Gln B:129 -Pro B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MQY)

(-) 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:338
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length: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        
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.hhhhh.eee............eeehhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhh.hhhhhh.....hhhhhhhhhhhhhhh....hhh.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhhh....................eee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqy A   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
                                    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        


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length: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        
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------Bse634I-3mqyB01 B:48-332                                                                                                                                                                                                                                                                     ------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------Bse634I-3mqyB02 B:48-332                                                                                                                                                                                                                                                                     ------- Pfam domains (2)
         Sec.struct. author ....hhhhhhh.hhhhh.eee............eeehhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhh...........eeeee.hhhhh.hhhhhh.....hhhhhhhhhhhhhhhh...hhh.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeee....hhhhhh...hhhhhhhh..........ee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqy B   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
                                    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        


Chain C from PDB  Type:DNA  Length:7
                                       
                 3mqy C   1 GAGTCCA   7


Chain D from PDB  Type:DNA  Length:11
                                           
                 3mqy D   8 CCGGTGGACTC  18
                                    17 


Chain E from PDB  Type:DNA  Length:7
                                       
                 3mqy E   1 GAGTCCA   7


Chain F from PDB  Type:DNA  Length:11
                                           
                 3mqy F   8 CCGGTGGACTC  18
                                    17
   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 3MQY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Bse634I] (5)

(-) 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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9F6L0_STRGR | Q9F6L0: 3dpg 3dvo 3dw9 3mq6 3n78 3n7b 4c3g

(-) Related Entries Specified in the PDB File

3dpg SGRAI WITH NONCOGNATE DNA BOUND
3dvo SGRAI WITH COGNATE DNA AND CALCIUM BOUND
3dw9 SGRAI WITH COGNATE DNA AND MANGANESE BOUND
3mq6 DOMAIN SWAPPED SGRAI WITH DNA AND CALCIUM BOUND