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(-) Description

Title :  RNASE II
 
Authors :  C. Frazao, C. E. Mcvey, M. Amblar, A. Barbas, C. Vonrhein, C. M. Arraiano M. A. Carrondo
Date :  05 Jul 06  (Deposition) - 05 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A
Keywords :  S1, Rna, Csd, Rnb, Nuclease, Rnase Ii, Hydrolase, Rna- Binding, Exonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Frazao, C. E. Mcvey, M. Amblar, A. Barbas, C. Vonrhein, C. M. Arraiano, M. A. Carrondo
Unravelling The Dynamics Of Rna Degradation By Ribonuclease Ii And Its Rna-Bound Complex
Nature V. 7 443 2006
PubMed-ID: 16957732  |  Reference-DOI: 10.1038/NATURE05080
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXORIBONUCLEASE 2
    ChainsA
    EC Number3.1.13.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    FragmentRESIDUES 6-644
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainC600
    SynonymRNASE II, EXORIBONUCLEASE II, RIBONUCLEASE II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CA1Ligand/IonCALCIUM ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:201 , ASP A:210 , HOH A:2055 , HOH A:2059 , HOH A:2060BINDING SITE FOR RESIDUE MG A1646
2AC2SOFTWAREPRO A:101 , HIS A:103 , LEU A:106 , HOH A:2004 , HOH A:2020 , HOH A:2021BINDING SITE FOR RESIDUE CA A1647
3AC3SOFTWAREPHE A:82 , PHE A:86 , VAL A:87 , PRO A:101 , ASP A:102 , HIS A:103 , ARG A:167BINDING SITE FOR RESIDUE C5P A1645

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IX0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IX0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IX0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_IIPS01175 Ribonuclease II family signature.RNB_ECOLI484-508  1A:484-508

(-) Exons   (0, 0)

(no "Exon" information available for 2IX0)

(-) 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:637
 aligned with RNB_ECOLI | P30850 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:641
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643 
            RNB_ECOLI     4 DNPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA 644
               SCOP domains d2ix0a2 A:4-82 Exoribonucle  ase 2, RNB                                        d2ix0a1 A:83-172 Exoribonuclease 2, RNB                                                   d2ix0a4 A:173-557 Exoribonuclease 2, RNB                                                                                                                                                                                                                                                                                                                                                         d2ix0a3 A:558-644 Exoribonuclease 2, RNB                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeee...--.eeeeee..eeeeehhhhhh......eeeeeee..--..eeeeeeeee....eeeeeee.....eeeee........eeeee............eeeeeeeehhhhh....eeeeeee.......hhhhhhhhhhh.....................ee.......eee........eeeeeeeehhheeeeeeee.hhhhh....hhhhhhhhhhh..eee..eee...hhhhhhh........eeeeeeeeeee..........eeeeeeee...eeehhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eee......................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeee.....eeeee.hhh..hhh.eeee....eeee..eeeee...eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_II          ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ix0 A   4 DDPLLAQLKQQLHSQTPRAEGVVKATE--FGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSE--RESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA 644
                                    13        23      | 33        43        53        63   |  | 73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643 
                                                     30 33                                67 70                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IX0)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNB_ECOLI | P30850)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0008859    exoribonuclease II activity    Catalysis of the reaction: RNA + H2O = 5'-phosphomononucleotides. Cleaves RNA in the 3' to 5' direction.
    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: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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    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:0016070    RNA metabolic process    The cellular chemical reactions and pathways involving 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:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000178    exosome (RNase complex)    A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNB_ECOLI | P308502id0 2ix1

(-) Related Entries Specified in the PDB File

2ix1 RNASE II D209N MUTANT