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(-) Description

Title :  SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN
 
Authors :  J. M. Perez-Canadillas, R. Campos-Olivas, J. Santoro, J. Lacadena, A. Martinez Del Pozo, J. G. Gavilanes, M. Rico, M. Bruix
Date :  12 Nov 99  (Deposition) - 21 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Alpha-Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Perez-Canadillas, J. Santoro, R. Campos-Olivas, J. Lacadena, A. Martinez Del Pozo, J. G. Gavilanes, M. Rico, M. Bruix
The Highly Refined Solution Structure Of The Cytotoxic Ribonuclease Alpha-Sarcin Reveals The Structural Requirements For Substrate Recognition And Ribonucleolytic Activity.
J. Mol. Biol. V. 299 1061 2000
PubMed-ID: 10843858  |  Reference-DOI: 10.1006/JMBI.2000.3813
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE ALPHA-SARCIN
    Chains: A
    EC Number: 3.1.27.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PINPGAS
    Expression System Taxid: 562
    Organism Scientific: ASPERGILLUS GIGANTEUS
    Organism Taxid: 5060
    Strain: MDH 18894

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DE3)

(-) Sites  (0, 0)

(no "Site" information available for 1DE3)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:6 -A:148
2A:76 -A:132

(-) Cis Peptide Bonds  (3, 60)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:48 -Pro A:49
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Lys A:112 -Pro A:113
31, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:126 -Pro A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DE3)

(-) Exons   (0, 0)

(no "Exon" information available for 1DE3)

(-) Sequences/Alignments

NMR Structure
   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:150
 aligned with RNAS_ASPGI | P00655 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:150
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177
           RNAS_ASPGI    28 AVTWTCLNDQKNPKTNKYETKRLLYNQNKAESNSHHAPLSDGKTGSSYPHWFTNGYDGDGKLPKGRTPIKFGKSDCDRPPKHSKDGNGKTDHYLLEFPTFPDGHDYKFDSKKPKENPGPARVIYTYPNKVFCGIIAHTKENQGELKLCSH 177
               SCOP domains d1de3a_ A: alpha-Sarcin                                                                                                                                SCOP domains
               CATH domains 1de3A00 A:1-150  [code=3.10.450.30, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeeehhhhhhhh...............ee...........................................eee.......................eeee......eeeeeee.......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1de3 A   1 AVTWTCLNDQKNPKTNKYETKRLLYNQNKAESNSHHAPLSDGKTGSSYPHWFTNGYDGDGKLPKGRTPIKFGKSDCDRPPKHSKDGNGKTDHYLLEFPTFPDGHDYKFDSKKPKENPGPARVIYTYPNKVFCGIIAHTKENQGELKLCSH 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DE3)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (RNAS_ASPGI | P00655)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0033902    rRNA endonuclease activity    Catalysis of the hydrolysis of the phosphodiester linkage between guanosine and adenosine residues at one specific position in 28S rRNA from rat ribosomes.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  Sites
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  Cis Peptide Bonds
    Lys A:112 - Pro A:113   [ RasMol ]  
    Tyr A:126 - Pro A:127   [ RasMol ]  
    Tyr A:48 - Pro A:49   [ RasMol ]  
 

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 Related Entries

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UniProtKB/Swiss-Prot
        RNAS_ASPGI | P00655: 1r4y

(-) Related Entries Specified in the PDB File

4158 15N AND 1H CHEMICAL SHIFTS