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(-) Description

Title :  THERMOVIBRIO AMMONIFICANS RNASE H3 IN COMPLEX WITH 19-MER RNA/DNA
 
Authors :  M. Figiel, M. Nowotny
Date :  26 Mar 14  (Deposition) - 30 Jul 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rnase H Fold, Rna/Dna Hybrid, Hydrolase-Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Figiel, M. Nowotny
Crystal Structure Of Rnase H3-Substrate Complex Reveals Parallel Evolution Of Rna/Dna Hybrid Recognition.
Nucleic Acids Res. V. 42 9285 2014
PubMed-ID: 25016521  |  Reference-DOI: 10.1093/NAR/GKU615

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21 STAR
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: THEAM_0945
    Mutation: YES
    Organism Scientific: THERMOVIBRIO AMMONIFICANS
    Organism Taxid: 648996
    Strain: HB-1
 
Molecule 2 - 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP *C)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP *C)-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, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3SO47Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:78 , GLU A:79 , HOH A:406 , HOH A:425 , G B:7 , A B:8BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREARG A:74 , ARG A:198 , ARG A:202 , HOH A:429 , HOH A:500 , HOH A:501BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREHIS A:132 , GLY A:133 , LYS A:250 , HOH A:421 , HOH A:460BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARESER A:5 , LYS A:8 , GLY A:196 , HOH A:508BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARELYS A:53 , GLY A:54 , ARG A:55BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWAREASN A:154 , ARG A:155 , ASN A:184 , ARG A:185 , DC C:17 , HOH C:218BINDING SITE FOR RESIDUE SO4 A 306
7AC7SOFTWAREPRO A:252 , LYS A:253BINDING SITE FOR RESIDUE SO4 A 307
8AC8SOFTWAREHIS A:28 , LYS A:44 , LEU A:199BINDING SITE FOR RESIDUE GOL A 308
9AC9SOFTWAREDC C:15 , DA C:16 , HOH C:211 , HOH C:216 , HOH C:217 , HOH C:221BINDING SITE FOR RESIDUE SO4 C 101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:100 -A:131

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:72 -Pro A:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PY5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PY5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PY5)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..eee.....eeeeeee..eeeeee....eeeee..hhhhhhhhhhhhhhh....eeeeeee........eeeeeeeehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhheeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py5 A   0 SMKLSSSEKEKLLKKLKALGAKEEKPPEHAQYRLRLNDAILTVYKSGSVVYGGKGREKLKELVAETVLSDTELPRIGCNEAGKGEFVGPLVVACIVADEKCLKRLIELGVKDSKKLSNEKVEELASEITETCHGKVKLLIPEKYNRAYSKFKNINRLLEAVYREIVSDLCEKFSPKVVVVDKFSNRAEEVLKDVVKGARLEVRPKAEDDLAVAAASIVAKAVRLKTMKELEKRFKVKLPEGNTGLAELLKKTPKELHEKLFKLHFSV 266
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       


Chain B from PDB  Type:RNA  Length:19
                                                   
                 4py5 B   1 GAGUGCGACACCUGAUUCC  19
                                    10         


Chain C from PDB  Type:DNA  Length:19
                                                   
                 4py5 C   1 GGAATCAGGTGTCGCACTC  19
                                    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 4PY5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PY5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PY5)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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