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(-) Description

Title :  CRYSTAL STRUCTURE OF LC11-RNASE H1 IN COMPLEX WITH RNA/DNA HYBRID
 
Authors :  T. N. Nguyen, D. J. You, H. Matsumoto, E. Kanaya, S. Kanaya
Date :  23 Sep 12  (Deposition) - 25 Sep 13  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rnase H, Ribonuclease H Rna Dna Hybrid, Hydrolase, Ribonuclease H, Hydrolase-Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Nguyen, D. J. You, H. Matsumoto, E. Kanaya, Y. Koga, S. Kanaya
Crystal Structure Of Metagenome-Derived Lc11-Rnase H1 In Complex With Rna/Dna Hybrid
J. Struct. Biol. V. 182 144 2013
PubMed-ID: 23500886  |  Reference-DOI: 10.1016/J.JSB.2013.02.018

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A, B
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET25B
    Expression System Strain: MIC2067(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: UNCULTURED ORGANISM
    Organism Taxid: 155900
    Synonym: LC11-RNASE H1
 
Molecule 2 - RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3')
    Chains: C
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN BACTERIA
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3')
    Chains: D
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN BACTERIA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4H8K)

(-) Sites  (0, 0)

(no "Site" information available for 4H8K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H8K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:15 -Pro A:16
2Asn B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H8K)

(-) Exons   (0, 0)

(no "Exon" information available for 4H8K)

(-) 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    
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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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h8k A   3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMNSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        


Chain B from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h8k B   3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMNSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        


Chain C from PDB  Type:RNA  Length:14
                                              
                 4h8k C   1 CGACACCUGAUUCC  14
                                    10    


Chain D from PDB  Type:DNA  Length:14
                                              
                 4h8k D   1 GGAATCAGGTGTCG  14
                                    10
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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  (0, 0)

(no "SCOP Domain" information available for 4H8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H8K)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Sites" information available for 4h8k)
 
  Cis Peptide Bonds
    Asn A:15 - Pro A:16   [ RasMol ]  
    Asn B:15 - Pro B:16   [ RasMol ]  
 

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