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(-) Description

Title :  B. HALODURANS RNASE H CATALYTIC DOMAIN E188A MUTANT IN COMPLEX WITH MG2+ AND RNA/DNA HYBRID (NON-P NICK AT THE ACTIVE SITE)
 
Authors :  M. Nowotny, W. Yang
Date :  02 Mar 06  (Deposition) - 25 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rnase H, Ribonuclease H Rna/Dna Hybrid, Hydrolase/Rna/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nowotny, W. Yang
Stepwise Analyses Of Metal Ions In Rnase H Catalysis From Substrate Destabilization To Product Release.
Embo J. V. 25 1924 2006
PubMed-ID: 16601679  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601076
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*GP*AP*CP*A)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*TP*GP*TP*CP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RIBONUCLEASE H
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 PLYSS
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: BH-RNASE HC
    Gene: RNHA
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Synonym: RNASE H

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , GLU A:109 , ASP A:132 , MG A:302 , A B:6 , HOH B:11BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREASP A:71 , ASP A:192 , MG A:301 , HOH A:402 , HOH A:404 , HOH A:457 , HOH B:11BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWARETYR A:83BINDING SITE FOR RESIDUE CL A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G8F)

(-) 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 2G8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G8F)

(-) Exons   (0, 0)

(no "Exon" information available for 2G8F)

(-) 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:133
 aligned with RNH1_BACHD | Q9KEI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:133
                                    70        80        90       100       110       120       130       140       150       160       170       180       190   
           RNH1_BACHD    61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY 193
               SCOP domains d2g8fa1 A:61-193 BH0863-like Ribonuclease H                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeee...eeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.......eee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g8f A  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGAIKADY 193
                                    70        80        90       100       110       120       130       140       150       160       170       180       190   


Chain B from PDB  Type:RNA  Length:6
                                      
                 2g8f B   1 UCGACA   6


Chain C from PDB  Type:DNA  Length:6
                                      
                 2g8f C   1 ATGTCG   6
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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 2G8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G8F)

(-) 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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  2g8f
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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 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 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

1zbf 1zbi 1zbl