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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE HII (EC 3.1.26.4) (RNASE HII) (TM0915) FROM THERMOTOGA MARITIMA AT 1.74 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  27 Oct 05  (Deposition) - 08 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Tm0915, Ribonuclease Hii (Ec 3. 1. 26. 4) (Rnase Hii), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Ribonuclease Hii (Ec 3. 1. 26. 4) (Rnase Hii) (Tm0915) From Thermotoga Maritima At 1. 74 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEASE HII
    Chains: A
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNHB
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RNASE HII

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:18 , ASP A:107 , HOH A:395 , HOH A:396 , HOH A:397 , HOH A:398BINDING SITE FOR RESIDUE MG A 239
2AC2SOFTWAREILE A:206 , SER A:207 , ARG A:210BINDING SITE FOR RESIDUE CL A 240
3AC3SOFTWARELYS A:9 , ILE A:71 , GLU A:76 , ARG A:92 , HOH A:318BINDING SITE FOR RESIDUE EDO A 241
4AC4SOFTWAREPHE A:83 , LYS A:87 , GLY A:110 , ARG A:198 , HOH A:292 , HOH A:339 , HOH A:358BINDING SITE FOR RESIDUE EDO A 242
5AC5SOFTWAREVAL A:104 , ILE A:111 , LEU A:113 , VAL A:115 , GLY A:117 , HOH A:316 , HOH A:364BINDING SITE FOR RESIDUE EDO A 243
6AC6SOFTWARESER A:184 , GLU A:202 , ARG A:213BINDING SITE FOR RESIDUE EDO A 244
7AC7SOFTWARELYS A:166 , LEU A:169 , ASN A:170 , ARG A:173 , HOH A:357BINDING SITE FOR RESIDUE EDO A 245

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ETJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ETJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ETJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ETJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2ETJ)

(-) 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:211
 aligned with RNH2_THEMA | Q9X017 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
           RNH2_THEMA     1 MGIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIEGINDSKQLSPAKRERLLDEIMEKAAVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRLSFEPVLELLTDDLLREFFEKGLISENRFERILNLLGAR 221
               SCOP domains d2etja1 A:1-221 Class II ribonuclease H (          RNase HII)                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....eeeeeee........eeeeeeee.....----------hhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhh........hhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2etj A   1 mGIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIE----------AKRERLLDEImEKAAVGIGIASPEEIDLYNIFNATKLAmNRALENLSVKPSFVLVDGKGIELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLmSEFHRmYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRLSFEPVLELLTDDLLREFFEKGLISENRFERILNLLGAR 221
                            |       10        20        30        40|        - |      60 |      70        80        90       100       110       120       130       140    |  150|      160       170       180       190       200       210       220 
                            |                                      41         52        62-MSE                      90-MSE                                                145-MSE |                                                                      
                            1-MSE                                                                                                                                               151-MSE
   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 2ETJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ETJ)

(-) 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: 3o3f 3o3g 3o3h 4hht

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