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(-) Description

Title :  THE STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA (BULLFROG)
 
Authors :  S. -S. Chern, F. N. Musayev, I. R. Amiraslanov, Y. -D. Liao, Y. -C. Liaw
Date :  14 Dec 01  (Deposition) - 09 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Rc-Rnase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. -S. Chern, F. N. Musayev, I. R. Amiraslanov, Y. -D. Liao, Y. -C. Liaw
The Structure Of A Cytotoxic Ribonuclease From The Oocyte Of Rana Catesbeiana (Bullfrog)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE, OOCYTES
    Chains: A
    EC Number: 3.1.27.5
    Organism Common: BULLFROG
    Organism Scientific: RANA CATESBEIANA
    Organism Taxid: 8400
    Other Details: OOCYTES
    Synonym: RC-RNASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:9 , HIS A:10 , LYS A:35 , HIS A:103 , PHE A:104 , HOH A:848BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWARESER A:44 , ALA A:45 , THR A:46 , ARG A:65 , HOH A:673 , HOH A:722BINDING SITE FOR RESIDUE PO4 A 502
3AC3SOFTWAREGLN A:33 , ARG A:73 , HOH A:613 , HOH A:713BINDING SITE FOR RESIDUE PO4 A 503

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:71
2A:34 -A:81
3A:52 -A:96
4A:93 -A:110

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:79 -Pro A:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KM9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNASO_LITCT56-62  1A:34-40

(-) Exons   (0, 0)

(no "Exon" information available for 1KM9)

(-) 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:111
 aligned with RNASO_LITCT | P11916 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:111
                                    32        42        52        62        72        82        92       102       112       122       132 
          RNASO_LITCT    23 QNWATFQQKHIINTPIINCNTIMDNNIYIVGGQCKRVNTFIISSATTVKAICTGVINMNVLSTTRFQLNTCTRTSITPRPCPYSSRTETNYICVKCENQYPVHFAGIGRCP 133
               SCOP domains d1km9a_ A: Amphibian cytotoxic ribonuclease                                                                     SCOP domains
               CATH domains -1km9A00 A:2-111 P-30 Protein                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhee.....hhhhhh.hhh.ee..ee..eeeeee.hhhhhhhhhh...eeeee....eeeeeeee.........eeeeeeee.eeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------RNASE_P----------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1km9 A   1 xNWATFQQKHIINTPIINCNTIMDNNIYIVGGQCKRVNTFIISSATTVKAICTGVINMNVLSTTRFQLNTCTRTSITPRPCPYSSRTETNYICVKCENQYPVHFAGIGRCP 111
                            |       10        20        30        40        50        60        70        80        90       100       110 
                            |                                                                                                              
                            1-PCA
   Legend:   → Mismatch (orange background)
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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) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KM9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNASO_LITCT | P11916)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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: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: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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  3.1.27.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNASO_LITCT | P11916: 1bc4 1km8 1m07

(-) Related Entries Specified in the PDB File

1bc4 1BC4 CONTAINS THE SAME PROTEIN
1km8 1KM8 CONTAINS THE SAME PROTEIN