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(-) Description

Title :  NATIVE T4 RNASE H IN THE ABSENCE OF DIVALENT METAL IONS
 
Authors :  S. J. Tomanicek, T. C. Mueser
Date :  29 Apr 09  (Deposition) - 12 May 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Bpt4 Rnase H, 5'-3' Exonuclease, Endonuclease, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Tomanicek, J. M. Devos, T. C. Mueser
Additional Order Appears In The Absence Of Metals In A Fen-1 Protein: Structural Analysis Of Magnesium Binding To Bacteriophage T4 Rnaseh
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNN2202
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 33.2, DAS, RNH
    Organism Common: BACTERIOPHAGE T4
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Strain: T4D
    Synonym: RNASE H

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:115 , LYS A:116 , MET A:119 , TYR A:121 , TYR A:278 , PRO A:281BINDING SITE FOR RESIDUE NA A 306
2AC2SOFTWAREARG A:215 , GLU A:217 , GLY A:218 , ARG A:220BINDING SITE FOR RESIDUE SO4 A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H8J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H8J)

(-) Exons   (0, 0)

(no "Exon" information available for 3H8J)

(-) 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:297
 aligned with RNH_BPT4 | P13319 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:297
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       
             RNH_BPT4     9 EDYKEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
               SCOP domains d3h8ja1 A:9-180 T4 RNase H                                                                                                                                                  --d3h8ja2 A:183-305 T4 RNase H                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeee.....hhhhh....eeeee....eee.....hhhhhhhhhhhhhhhhhh........hhhhhh.........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h8j A   9 EDYKEGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDNVASVKVRSDFWFTRVEGERTPSMKTSIVEAIANDREQAKVLLTESEYNRYKENLVLIDFDYIPDNIASNIVNYYNSYKLPPRGKIYSYFVKAGLSKLTNSINEF 305
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H8J)

(-) 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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  3.1.26.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNH_BPT4 | P13319: 1tfr 2ihn 3h7i 3h8s 3h8w

(-) Related Entries Specified in the PDB File

1tfr RNASE H FROM BACTERIOPHAGE T4
2ihn CO-CRYSTAL OF BACTERIOPHAGE T4 RNASE H WITH A FORK DNA SUBSTRATE
3h7i METAL-FREE D132N T4 RNASE H
3h8s
3h8w