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(-) Description

Title :  T. MARITIMA RNASE H2 D107N IN COMPLEX WITH NUCLEIC ACID SUBSTRATE AND MANGANESE IONS
 
Authors :  M. P. Rychlik, H. Chon, S. M. Cerritelli, P. Klimek, R. J. Crouch, M. Nowo
Date :  24 Jul 10  (Deposition) - 08 Dec 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Rnase H Fold, Nuclease, Hydrolase-Dna-Rna Hybrid Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. P. Rychlik, H. Chon, S. M. Cerritelli, P. Klimek, R. J. Crouch, M. Nowotny
Crystal Structures Of Rnase H2 In Complex With Nucleic Acid Reveal The Mechanism Of Rna-Dna Junction Recognition And Cleavage.
Mol. Cell V. 40 658 2010
PubMed-ID: 21095591  |  Reference-DOI: 10.1016/J.MOLCEL.2010.11.001

(-) Compounds

Molecule 1 - RIBONUCLEASE HII
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNHB, TM_0915
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    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
    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
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , HOH A:246 , C D:6BINDING SITE FOR RESIDUE MN A 1
2AC2SOFTWAREASP A:18 , ASP A:45 , ASP A:124 , HOH A:253 , C D:6 , DT D:7BINDING SITE FOR RESIDUE MN A 224
3AC3SOFTWAREDG C:10BINDING SITE FOR RESIDUE MN C 13

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O3H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O3H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O3H)

(-) Exons   (0, 0)

(no "Exon" information available for 3O3H)

(-) 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:222
 aligned with RNH2_THEMA | Q9X017 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
           RNH2_THEMA     2 GIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIEGINDSKQLSPAKRERLLDEIMEKAAVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRLSFEPVLELLTDDLLREFFEKGLISENRFERILNLLGARKS 223
               SCOP domains d3o3ha_ A: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------RNase_HII-3o3hA01 A:15-188                                                                                                                                                    ----------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeee........eeeeeeee........hhhhhhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o3h A   2 GIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIEGINDSKQLSPAKRERLLDEIMEKAAVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVNGKGIELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRLSFEPVLELLTDDLLREFFEKGLISENRFERILNLLGARKS 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  


Chain C from PDB  Type:DNA  Length:12
                                            
                 3o3h C   1 GAATCAGGTGTC  12
                                    10  


Chain D from PDB  Type:DNA/RNA  Length:12
                                            
                 3o3h D   1 GACACCTGATTC  12
                                    10
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O3H)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNH2_THEMA | Q9X017)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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:0043137    DNA replication, removal of RNA primer    Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    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:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    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.
    GO:0032299    ribonuclease H2 complex    A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNH2_THEMA | Q9X017: 2etj 3o3f 3o3g 4hht

(-) Related Entries Specified in the PDB File

2etj APO STRUCTURE OF T. MARITIMA RNASE H2
3o3f T. MARITIMA RNASE H2 D107N IN COMPLEX WITH NUCLEIC ACID SUBSTRATE AND MAGNESIUM IONS
3o3g T. MARITIMA RNASE H2 IN COMPLEX WITH NUCLEIC ACID SUBSTRATE AND CALCIUM IONS