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(-) Description

Title :  RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH PRODUCT DNA
 
Authors :  M. Sokolowska, H. Czapinska, M. Bochtler
Date :  06 Sep 10  (Deposition) - 20 Oct 10  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Endonuclease-Dna Complex, Restriction Enzyme, Hpy188I, Intercalation, Giy-Yig Nuclease, Catalytic Mechanism, Pseudopalindrome, Hydrolase- Dna Complex, Restriction Endonuclease, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sokolowska, H. Czapinska, M. Bochtler
Hpy188I-Dna Pre- And Post-Cleavage Complexes--Snapshots Of The Giy-Yig Nuclease Mediated Catalysis.
Nucleic Acids Res. V. 39 1554 2011
PubMed-ID: 20935048  |  Reference-DOI: 10.1093/NAR/GKQ821

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE HPY188I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15BMOD
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HPY188IR, SYNTHETIC GENE CODON OPTIMIZED FOR ESCHERICHIA COLI
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 585532
    Strain: 188
 
Molecule 2 - 5'-D(*GP*AP*TP*CP*T)-3'
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*TP*TP*CP*A)-3'
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 4 - 5'-D(P*GP*AP*AP*C)-3'
    Chains: E
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 5 - 5'-D(P*GP*AP*TP*C)-3'
    Chains: F
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1AUTHORGLU A:149 , HIS B:76 , DA D:0 , DG F:1 , HOH D:53 , HOH F:39BINDING SITE FOR RESIDUE CA A 171, CONFORMER A
02AC2AUTHORGLU B:149 , HIS A:76 , DT C:0 , DG E:1 , HOH C:358 , HOH F:52BINDING SITE FOR RESIDUE CA A 172, CONFORMER A
03AC3AUTHORASP A:18 , ASP B:18 , HOH A:218 , HOH A:219 , HOH A:221 , HOH A:222BINDING SITE FOR RESIDUE CA A 173
04AC4AUTHORASN A:159 , HIS A:160 , GLU B:26 , HOH A:210BINDING SITE FOR RESIDUE CL A 174
05AC5AUTHORSER B:143 , HOH B:201 , HOH B:230 , HOH A:178BINDING SITE FOR RESIDUE CL A 175, CONFORMER A
06AC7AUTHORGLU A:26 , ASN B:159 , HIS B:160 , HOH B:176BINDING SITE FOR RESIDUE CL B 171
07BC1AUTHORGLU A:149 , HIS B:76 , DT C:0 , DG E:1 , HOH D:53 , HOH F:39BINDING SITE FOR RESIDUE CA A 171, CONFORMER B
08BC2AUTHORGLU B:149 , HIS A:76 , DA D:0 , DG F:1 , HOH C:358 , HOH F:52BINDING SITE FOR RESIDUE CA A 172, CONFORMER B
09BC5AUTHORSER A:143 , HOH A:276 , HOH E:183 , HOH B:181BINDING SITE FOR RESIDUE CL A 175, CONFORMER B
10BC6AUTHORLYS A:92 , HOH D:323BINDING SITE FOR RESIDUE CL A 176

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OR3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OR3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OR3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OR3)

(-) Exons   (0, 0)

(no "Exon" information available for 3OR3)

(-) 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:173
 aligned with Q9KJ88_HELPX | Q9KJ88 from UniProtKB/TrEMBL  Length:170

    Alignment length:173
                               1                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
         Q9KJ88_HELPX     - ---MAKRKSDIILKSVDDLKDEIDYKDFEYKEYFNLLCELVPNNSLEKLEINAIDEKNMKNEGLVYVFVIQGKIFKIGHSITPITKRVQSYNCGKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKTYQDSFSTSKRAENVILENFIKNHNKKPIGCTQT 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh...hhhhhh...hhhhh.hhhhheeeeeeeee....eeeeee.hhhhh....eeeeeee..eeeeeeee..hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee......eee..eee....hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3or3 A  -2 HEFMAKRKSDIILKSVDDLKDEIDYKDFEYKEYFNLLCELVPNNSLEKLEINAIDEKNmKNEGLVYVFVIQGKIFKIGHSITPITKRVQSYNCGKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKTYQDSFSTSKRAENVILENFIKNHNKKPIGCTQT 170
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
                                                                                     56-MSE                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q9KJ88_HELPX | Q9KJ88 from UniProtKB/TrEMBL  Length:170

    Alignment length:173
                               1                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
         Q9KJ88_HELPX     - ---MAKRKSDIILKSVDDLKDEIDYKDFEYKEYFNLLCELVPNNSLEKLEINAIDEKNMKNEGLVYVFVIQGKIFKIGHSITPITKRVQSYNCGKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKTYQDSFSTSKRAENVILENFIKNHNKKPIGCTQT 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh...hhhhhh...hhhhh.hhhhheeeeeeeee....eeeeee.hhhhh....eeeeeee..eeeeeeee..hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee.....eeee..eeee...hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3or3 B  -2 HEFMAKRKSDIILKSVDDLKDEIDYKDFEYKEYFNLLCELVPNNSLEKLEINAIDEKNmKNEGLVYVFVIQGKIFKIGHSITPITKRVQSYNCGKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKTYQDSFSTSKRAENVILENFIKNHNKKPIGCTQT 170
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
                                                                                     56-MSE                                                                                                              


Chain C from PDB  Type:DNA  Length:5
                                     
                 3or3 C  -4 GATCT   0


Chain D from PDB  Type:DNA  Length:5
                                     
                 3or3 D  -4 GTTCA   0


Chain E from PDB  Type:DNA  Length:4
                                    
                 3or3 E   1 GAAC   4


Chain F from PDB  Type:DNA  Length:4
                                    
                 3or3 F   1 GATC   4
   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 3OR3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OR3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OR3)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3OR3)

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  3or3
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 Related Entries

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

UniProtKB/TrEMBL
        Q9KJ88_HELPX | Q9KJ88: 3oqg

(-) Related Entries Specified in the PDB File

1mk0 CATALYTIC DOMAIN OF INTRON ENDONUCLEASE I-TEVI, E75A MUTANT
1yd1 CRYSTAL STRUCTURE OF THE GIY-YIG N-TERMINAL ENDONUCLEASE DOMAIN OF UVRC FROM THERMOTOGA MARITIMA BOUND TO ITS CATALYTIC DIVALENT CATION: MAGNESIUM
2wsh STRUCTURE OF BACTERIOPHAGE T4 ENDOII E118A MUTANT
3mx1 THE STRUCTURE OF GIY-YIG ENDONUCLEASE R.ECO29KI
3mx4 DNA BINDING AND CLEAVAGE BY THE GIY-YIG ENDONUCLEASE R.ECO29KI INACTIVE VARIANT E142Q
3nic DNA BINDING AND CLEAVAGE BY THE GIY-YIG ENDONUCLEASE R.ECO29KI INACTIVE VARIANT Y49F
3oqg RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH SUBSTRATE DNA