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(-) Description

Title :  CO-CRYSTAL OF BACTERIOPHAGE T4 RNASE H WITH A FORK DNA SUBSTRATE
 
Authors :  J. M. Devos, T. C. Mueser
Date :  26 Sep 06  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Bpt4 Rnase H, Protein:Dna Complex, 5'-3' Exonuclease, Hydrolase (Nucleic Acid), Helix-Hairpin-Helix Motif Type 2 (Hhh2), Fork Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Devos, S. J. Tomanicek, C. E. Jones, N. G. Nossal, T. C. Mueser
Crystal Structure Of Bacteriophage T4 5' Nuclease In Complex With A Branched Dna Reveals How Fen-1 Family Nucleases Bind Their Substrates.
J. Biol. Chem. V. 282 31713 2007
PubMed-ID: 17693399  |  Reference-DOI: 10.1074/JBC.M703209200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*CP*TP*AP*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*CP*C)- 3'
    ChainsC
    EngineeredYES
    Other DetailsDNA WAS DESIGNED ACCORDING TO SEQUENCES IN HARRINGTON, J.J. AND LIEBER, M.R. EMBO J. 13, 1235-46 (1994)
    SyntheticYES
 
Molecule 2 - 5'- D(*GP*GP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*TP*AP *GP*TP*CP*AP*A)-3'
    ChainsD
    EngineeredYES
    Other DetailsDNA WAS DESIGNED ACCORDING TO SEQUENCES IN HARRINGTON, J.J. AND LIEBER, M.R. EMBO J. 13, 1235-46 (1994)
    SyntheticYES
 
Molecule 3 - RIBONUCLEASE H
    ChainsA
    EC Number3.1.26.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNN2202-D132N
    Expression System StrainBL21(DE3)-PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRNH, 33.2, DAS
    MutationYES
    Organism ScientificENTEROBACTERIA PHAGE T4
    Organism Taxid10665
    StrainT4D
    SynonymRNASE H

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2IHN)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Exons   (0, 0)

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(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:299
 aligned with RNH_BPT4 | P13319 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
             RNH_BPT4     1 MDLEMMLDEDYKEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
               SCOP domains -----------d2ihna2 A:12-180 T4 RNase H                                                                                                                                              --d2ihna1 A:183-305 T4 RNase H                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhh.......------...hhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh..eeee.............hhhhhhhhhhhhh............................hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ihn A   1 MDLEMMLDEDYKEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNR------STWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEANDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
                                    10        20        30        40        50        60        70        80        90      |100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
                                                                                                                    90     97                                                                                                                                                                                                                

Chain C from PDB  Type:DNA  Length:17
                                                 
                 2ihn C   2 TAACTTTGAGGCAGACC  18
                                    11       

Chain D from PDB  Type:DNA  Length:17
                                                 
                 2ihn D   1 GGTCTGCCTCAAGACGG  17
                                    10       

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IHN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IHN)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNH_BPT4 | P13319)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RNH_BPT4 | P133191tfr 3h7i 3h8j 3h8s 3h8w

(-) Related Entries Specified in the PDB File

1tfr WILD TYPE RNASE H FROM BACTERIOPHAGE T4 IN THE PRESENCE OF TWO HYDRATED MAGNESIUM IONS IN THE ACTIVE SITE