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(-) Description

Title :  BACILLUS HALODURANS RNASE H CATALYTIC DOMAIN MUTANT D192N IN COMPLEX WITH 12-MER RNA/DNA HYBRID
 
Authors :  M. Nowotny, S. A. Gaidamakov, R. J. Crouch, W. Yang
Date :  08 Apr 05  (Deposition) - 12 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D  (2x)
Biol. Unit 1:  A,B,C,D  (1x)
Keywords :  Rnase H, Rna/Dna Hybrid, Dde Motif, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nowotny, S. A. Gaidamakov, R. J. Crouch, W. Yang
Crystal Structures Of Rnase H Bound To An Rna/Dna Hybrid: Substrate Specificity And Metal-Dependent Catalysis.
Cell(Cambridge, Mass. ) V. 121 1005 2005
PubMed-ID: 15989951  |  Reference-DOI: 10.1016/J.CELL.2005.04.024

(-) Compounds

Molecule 1 - 5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RIBONUCLEASE H-RELATED PROTEIN
    Chains: A, B
    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
    Fragment: CATALYTIC DOMAIN (RESIDUES 59-196)
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: C-125

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit (2x): ABCD
Biological Unit 1 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , GLU A:109 , ASP A:132 , HOH A:206 , A C:4 , C C:5BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREASP A:71 , ASN A:192 , HOH A:203 , C C:5 , HOH C:14 , HOH C:19BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREASP B:71 , GLU B:109 , ASP B:132 , HOH B:205 , U C:10 , U C:11BINDING SITE FOR RESIDUE MG B 203
4AC4SOFTWAREASP B:71 , ASN B:192 , HOH B:215 , HOH B:232 , U C:11 , HOH C:59BINDING SITE FOR RESIDUE MG B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZBL)

(-) Cis Peptide Bonds  (2, 4)

Asymmetric Unit
No.ModelResidues
11, 2Asn A:77 -Pro A:78
21, 2Asn B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZBL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZBL)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZBL)

(-) Sequences/Alignments

Asymmetric 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 -d1zbla1 A:62-193 BH0863-like Ribonuclease H                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeee...eeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhh............hhhhhhhhhhhhhhhhh......eee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zbl A  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKANY 193
                                    70        80        90       100       110       120       130       140       150       160       170       180       190   


Chain B 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 d1zblb_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------RNase_H-1zblB01 B:69-176                                                                                    ----------------- Pfam domains (1)
           Pfam domains (2) --------RNase_H-1zblB02 B:69-176                                                                                    ----------------- Pfam domains (2)
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeee...eeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhh............hhhhhhhhhhhhhhhhh......eee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zbl B  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKANY 193
                                    70        80        90       100       110       120       130       140       150       160       170       180       190   


Chain C from PDB  Type:RNA  Length:12
                                            
                 1zbl C   1 GACACCUGAUUC  12
                                    10  


Chain D from PDB  Type:DNA  Length:12
                                            
                 1zbl D  13 GAATCAGGTGTC  24
                                    22
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZBL)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  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 2g8f 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 CRYSTAL STRCTURE OF B. HALODURANS RNASE H CATALYTIC DOMAIN MUTANT D132N
1zbi BACILLUS HALODURANS RNASE H CATALYTIC DOMAIN MUTANT D132N IN COMPLEX WITH 12-MER RNA/DNA HYBRID