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(-) Description

Title :  RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH SUBSTRATE DNA
 
Authors :  M. Sokolowska, H. Czapinska, M. Bochtler
Date :  03 Sep 10  (Deposition) - 20 Oct 10  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Endonuclease-Dna Complex, Restriction Enzyme, Hpy188I, Intercalation, Giy-Yig Nuclease, Catalytic Mechanism, Pseudopalindrome, Hydrolase- Dna Complex (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 - 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
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 585532
    Strain: 188
 
Molecule 2 - DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA2Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1AUTHORGLU A:149 , HOH A:238 , HOH A:276 , HOH B:203 , DA D:0 , DG D:1BINDING SITE FOR RESIDUE NA A 171, CONFORMER A
2AC2AUTHORASN A:159 , HIS A:160 , HOH A:307 , GLU B:26BINDING SITE FOR RESIDUE CL A 172
3AC3AUTHORGLU B:149 , HOH A:218 , HOH B:216 , HOH B:232 , DT C:0 , DG C:1BINDING SITE FOR RESIDUE NA B 171, CONFORMER A
4BC1AUTHORGLU A:149 , HOH A:238 , HOH A:276 , HOH B:203 , DT C:0 , DG C:1BINDING SITE FOR RESIDUE NA A 171, CONFORMER B
5BC3AUTHORGLU B:149 , HOH A:218 , HOH B:216 , HOH B:232 , DA D:0 , DG D:1BINDING SITE FOR RESIDUE NA B 171, CONFORMER B

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OQG)

(-) 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:176
 aligned with Q9KJ88_HELPX | Q9KJ88 from UniProtKB/TrEMBL  Length:170

    Alignment length:176
                                  1                                                                                                                                                                         
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164      
         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
                 3oqg A  -5 HHHHEFMAKRKSDIILKSVDDLKDEIDYKDFEYKEYFNLLCELVPNNSLEKLEINAIDEKNmKNEGLVYVFVIQGKIFKIGHSITPITKRVQSYNCGKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKTYQDSFSTSKRAENVILENFIKNHNKKPIGCTQT 170
                                     4        14        24        34        44        54 |      64        74        84        94       104       114       124       134       144       154       164      
                                                                                        56-MSE                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with Q9KJ88_HELPX | Q9KJ88 from UniProtKB/TrEMBL  Length:170

    Alignment length:175
                                 1                                                                                                                                                                         
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165     
         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
                 3oqg B  -4 HHHEFMAKRKSDIILKSVDDLKDEIDYKDFEYKEYFNLLCELVPNNSLEKLEINAIDEKNmKNEGLVYVFVIQGKIFKIGHSITPITKRVQSYNCGKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKTYQDSFSTSKRAENVILENFIKNHNKKPIGCTQT 170
                                     5        15        25        35        45        55|       65        75        85        95       105       115       125       135       145       155       165     
                                                                                       56-MSE                                                                                                              


Chain C from PDB  Type:DNA  Length:9
                                         
                 3oqg C  -4 GATCTGAAC   4


Chain D from PDB  Type:DNA  Length:9
                                         
                 3oqg D  -4 GTTCAGATC   4
   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 3OQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  3oqg
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  Q9KJ88_HELPX | Q9KJ88
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 Related Entries

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

UniProtKB/TrEMBL
        Q9KJ88_HELPX | Q9KJ88: 3or3

(-) 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
3or3 RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH PRODUCT DNA