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(-) Description

Title :  T. MARITIMA RNASE H2 G21S IN COMPLEX WITH NUCLEIC ACID SUBSTRATE AND CALCIUM IONS
 
Authors :  M. P. Rychlik, M. Nowotny
Date :  10 Oct 12  (Deposition) - 06 Feb 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Rnase H, Nuclease, Single Ribonucleotide Removal, Hydrolase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Chon, J. L. Sparks, M. Rychlik, M. Nowotny, P. M. Burgers, R. J. Crouch, S. M. Cerritelli
Rnase H2 Roles In Genome Integrity Revealed By Unlinking It Activities.
Nucleic Acids Res. V. 41 3130 2013
PubMed-ID: 23355612  |  Reference-DOI: 10.1093/NAR/GKT027

(-) Compounds

Molecule 1 - RIBONUCLEASE HII
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RNHB, TM_0915
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: RNASE HII
 
Molecule 2 - DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
    Chains: C
    Engineered: YES
    Other Details: 12-MER DNA
    Synthetic: YES
 
Molecule 3 - DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)- 3')
    Chains: D
    Engineered: YES
    Other Details: 12-MER DNA WITH SINGLE RIBONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , GLN A:125 , C D:6 , HOH D:104BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREASP A:18 , GLU A:19 , HOH A:410 , C D:6 , DT D:7 , HOH D:102BINDING SITE FOR RESIDUE CA A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HHT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HHT)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains d4hhta_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeeeee........eeeeeeee...........hhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhh........hhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hht A   2 GIDELYKKEFGIVAGVDEASRGCLAGPVVAAAVVLEKEIEGINDSRLLDEIMEKAAVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRLSFEPVLELLTDDLLREFFEKGLISENRFERILNLLGARKSVVFRKER 230
                                    11        21        31        41    ||  60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
                                                                       46|                                                                                                                                                                              
                                                                        56                                                                                                                                                                              


Chain C from PDB  Type:DNA  Length:12
                                            
                 4hht C   1 GAATCAGGTGTC  12
                                    10  


Chain D from PDB  Type:DNA/RNA  Length:12
                                            
                 4hht D   1 GACACCTGATTC  12
                                    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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hht
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  RNH2_THEMA | Q9X017
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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
        RNH2_THEMA | Q9X017: 2etj 3o3f 3o3g 3o3h

(-) Related Entries Specified in the PDB File

3o3f 3o3g 3o3h