Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  B. HALODURANS RNASE H CATALYTIC DOMAIN D192N MUTANT IN COMPLEX WITH MN2+ 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'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*AP*TP*GP*TP*CP*G)-3'
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - RIBONUCLEASE H
    ChainsA
    EC Number3.1.26.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 PLYSS
    Expression System Taxid562
    Expression System VectorPET15B
    Expression System Vector TypePLASMID
    FragmentBH-RNASE HC
    GeneRNHA
    MutationYES
    Organism ScientificBACILLUS HALODURANS
    Organism Taxid86665
    SynonymRNASE H

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MN4Ligand/IonMANGANESE (II) ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , GLU A:109 , ASP A:132 , MN A:402 , A B:6 , HOH B:61BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWAREASP A:71 , ASN A:192 , MN A:401 , HOH A:503 , HOH A:505 , HOH A:559 , HOH B:61BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREASP A:163 , GLU A:166 , HOH A:577 , HOH A:638 , HOH A:673 , HOH A:718BINDING SITE FOR RESIDUE MN A 403
4AC4SOFTWAREGLU A:82 , GLU A:96 , HOH A:605 , HOH A:648BINDING SITE FOR RESIDUE MN A 404
5AC5SOFTWARETYR A:83 , HOH A:550BINDING SITE FOR RESIDUE CL A 502
6AC6SOFTWAREHIS A:115 , ARG A:118 , TYR A:119 , GLU A:167 , HOH A:533 , HOH A:590BINDING SITE FOR RESIDUE MPD A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G8I)

(-) 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 2G8I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G8I)

(-) Exons   (0, 0)

(no "Exon" information available for 2G8I)

(-) 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
                                    71        81        91       101       111       121       131       141       151       161       171       181       191    
           RNH1_BACHD    62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGR 195
               SCOP domains d2g8ia_ A: BH0863-like Ribonuclease H                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.......eee.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g8i A  62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKANYGR 195
                                    71        81        91       101       111       121       131       141       151       161       171       181       191    

Chain B from PDB  Type:RNA  Length:6
                                      
                 2g8i B   1 UCGACA   6

Chain C from PDB  Type:DNA  Length:6
                                      
                 2g8i C   1 ATGTCG   6

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G8I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G8I)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:77 - Pro A:78   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2g8i
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RNH1_BACHD | Q9KEI9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.26.4
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RNH1_BACHD | Q9KEI9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RNH1_BACHD | Q9KEI91zbf 1zbi 1zbl 2g8f 2g8h 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 2g8f 2g8h