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(-) Description

Title :  X-RAY STRUCTURE OF M23L ONCONASE AT 298K
 
Authors :  A. Merlino, L. Mazzarella, A. Carannante, A. Di Fiore, A. Di Donato, E. Notomista, F. Sica
Date :  15 Feb 05  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Crystal Structure, Small Conformational Changes, Onconase Thermal Stability, Ribonucleases, Antitumor Action, Dynamics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merlino, L. Mazzarella, A. Carannante, A. Di Fiore, A. Di Donato, E. Notomista, F. Sica
The Importance Of Dynamic Effects On The Enzyme Activity: X-Ray Structure And Molecular Dynamics Of Onconase Mutants
J. Biol. Chem. V. 280 17953 2005
PubMed-ID: 15728177  |  Reference-DOI: 10.1074/JBC.M501339200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P-30 PROTEIN
    Chains: A
    EC Number: 3.1.27.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: NORTHERN LEOPARD FROG
    Organism Scientific: RANA PIPIENS
    Organism Taxid: 8404
    Synonym: ONCONASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:9 , HIS A:10 , LYS A:55 , HIS A:97 , PHE A:98 , HOH A:519 , HOH A:533 , HOH A:573BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:68
2A:30 -A:75
3A:48 -A:90
4A:87 -A:104

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YV6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNP30_LITPI30-36  1A:30-36

(-) Exons   (0, 0)

(no "Exon" information available for 1YV6)

(-) 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:104
 aligned with RNP30_LITPI | P22069 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
          RNP30_LITPI     1 QDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 104
               SCOP domains d1yv6a_ A: Amphibian cytotoxic ribonuclease                                                              SCOP domains
               CATH domains -1yv6A00 A:2-104 P-30 Protein                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhee.....hhhhhh.........eeeeee.hhhhhhhhhh.....eeee....eeeeeeee......eeeeeeee.eeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------RNASE_P-------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1yv6 A   1 xDWLTFQKKHITNTRDVDCDNILSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 104
                            |       10        20        30        40        50        60        70        80        90       100    
                            |                                                                                                       
                            1-PCA
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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 1YV6)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNP30_LITPI | P22069)
molecular function
    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.

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  1yv6
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  3.1.27.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNP30_LITPI | P22069: 1onc 1pu3 1yv4 1yv7 2gmk 2i5s 2kb6 2lt5 3fd7 3hg6 3phn 3snf 3u00 3u01

(-) Related Entries Specified in the PDB File

1yv4 THE SAME PROTEIN(M23L) AT 100K
1yv7 THE SAME PROTEIN(C87S,DES103-104) AT 298K