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(-) Description

Title :  SELENIUM DERIVATIZED RNA/DNA HYBRID IN COMPLEX WITH RNASE H CATALYTIC DOMAIN D132N MUTANT
 
Authors :  A. Rob, O. Gerlits, J. S. Jiang, J. H. Gan, Z. Huang
Date :  21 Sep 11  (Deposition) - 03 Oct 12  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Selenium-Dna/Rna, Rnase H, Endonuclease, Hydrolase, Magnesium, Manganese, Metal-Binding, Selenium-Modification, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Abdur, O. O. Gerlits, J. Gan, J. Jiang, J. Salon, A. Y. Kovalevsky, A. A. Chumanevich, I. T. Weber, Z. Huang
Novel Complex Mad Phasing And Rnase H Structural Insights Using Selenium Oligonucleotides.
Acta Crystallogr. , Sect. D V. 70 354 2014
PubMed-ID: 24531469  |  Reference-DOI: 10.1107/S1399004713027922

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: BH0863, RNHA
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Synonym: RNASE H
 
Molecule 2 - RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*TP*(SDG)P*TP*CP*(SDG))-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
3SDG2Mod. Nucleotide2-AMINO-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURINE-6-SELENOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:36 , HOH A:55 , ASP A:71 , ASP A:192 , C B:5 , HOH B:56BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:71 , GLU A:109 , ASN A:132 , A B:4 , C B:5BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARETRP A:139 , LYS A:146 , DA C:1 , SDG C:6 , HOH C:77 , HOH C:107BINDING SITE FOR RESIDUE PO4 C 7

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:77 -Pro A:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TWH)

(-) 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:134
 aligned with RNH1_BACHD | Q9KEI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:134
                                    70        80        90       100       110       120       130       140       150       160       170       180       190    
           RNH1_BACHD    61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
               SCOP domains d3twha_ A: BH0863-like Ribonuclease H                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhh.......eee.hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3twh A  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
                                    70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:RNA  Length:6
                                      
                 3twh B   1 UCGACA   6


Chain C from PDB  Type:DNA  Length:6
                                      
                 3twh C   1 ATgTCg   6
                              |  |
                              3-SDG
                                 6-SDG
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNH1_BACHD | Q9KEI9)
molecular function
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Asn A:77 - Pro A:78   [ RasMol ]  
 

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  3twh
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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
        RNH1_BACHD | Q9KEI9: 1zbf 1zbi 1zbl 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 3d0p 3ey1 3i8d 3uld 4htu 4hue 4huf 4hug 4opj 4opk 5swm 5us2 5usa 5use 5usg 5w7n 5w7o

(-) Related Entries Specified in the PDB File

1zbi BACILLUS HALODURANS RNASE H CATALYTIC DOMAIN MUTANT D132N IN COMPLEX WITH 12-MER RNA/DNA HYBRID
2g8u B. HALODURANS RNASE H CATALYTIC DOMAIN D132N MUTANT IN COMPLEX WITH MG2+ AND RNA/DNA HYBRID