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(-) Description

Title :  SELENIUM DERIVATIZED RNA/DNA HYBRID IN COMPLEX WITH RNASE H CATALYTIC DOMAIN MUTANT D132N
 
Authors :  J. -S. Jiang, O. Gerlits, Z. Huang
Date :  10 Sep 07  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Selenium-Dna/Rna, Rnase H, Ribonuclease H Rna/Dna Complex, Cytoplasm, Endonuclease, Hydrolase, Magnesium, Manganese, Metal-Binding, Hydrolase/Rna/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -S. Jiang, O. Gerlits, Z. Huang
Selenium Derivatized Rna/Dna Hybrid In Complex With Rnase H Catalytic Domain Mutant D132N
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 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(*DAP*DTP*(SDG)P*DTP*DCP*(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
1AC1SOFTWARETRP A:139 , LYS A:146 , DA C:1 , HOH C:50 , HOH C:134 , HOH C:148BINDING SITE FOR RESIDUE PO4 C 7
2AC2SOFTWAREASP A:71 , GLU A:109 , ASN A:132 , HOH A:412BINDING SITE FOR RESIDUE MG A 401
3AC3SOFTWAREASP A:71 , ASP A:192 , HOH A:403 , HOH A:404 , HOH A:405BINDING SITE FOR RESIDUE MG A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R7Y)

(-) 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 2R7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2R7Y)

(-) 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:132
 aligned with RNH1_BACHD | Q9KEI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:132
                                    71        81        91       101       111       121       131       141       151       161       171       181       191  
           RNH1_BACHD    62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY 193
               SCOP domains d2r7ya_ A: BH0863-like Ribonuclease H                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------RNase_H-2r7yA01 A:69-176                                                                                    ----------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhh.......eee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r7y A  62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY 193
                                    71        81        91       101       111       121       131       141       151       161       171       181       191  


Chain B from PDB  Type:RNA  Length:6
                                      
                 2r7y B   1 UCGACA   6


Chain C from PDB  Type:DNA  Length:6
                                      
                 2r7y 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 2R7Y)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) 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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 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 3d0p 3ey1 3i8d 3twh 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