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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RECOMBINANT ONCONASE FROM RANA PIPIENS
 
Authors :  A. Camara-Artigas, J. A. Gavira, S. Casares-Atienza, U. Weininger, J. M. M. Garcia-Mira
Date :  13 May 09  (Deposition) - 19 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha And Beta Protein, Endonuclease, Hydrolase, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Casares-Atienza, U. Weininger, A. Camara-Artigas, J. Balbach, M. M. Garcia-Mira
Re-Examination Of Onconase Thermal Unfolding Mechanism
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ONCONASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPR
    Organism Scientific: RANA PIPIENS
    Organism Taxid: 8404

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPCA A:1 , LYS A:9 , HIS A:10 , LYS A:55 , HIS A:97 , PHE A:98 , HOH A:134BINDING SITE FOR RESIDUE SO4 A 105
2AC2SOFTWAREASN A:13 , THR A:71 , SER A:72 , LYS A:78BINDING SITE FOR RESIDUE SO4 A 106
3AC3SOFTWARETRP A:3 , LYS A:45 , HOH A:183 , HOH A:191BINDING SITE FOR RESIDUE SO4 A 107
4AC4SOFTWAREARG A:15 , LYS A:81 , GLU A:91BINDING SITE FOR RESIDUE SO4 A 108
5AC5SOFTWAREHIS A:29 , ASN A:56 , HOH A:139 , HOH A:192BINDING SITE FOR RESIDUE GOL A 109

(-) 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 3HG6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HG6)

(-) 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 3HG6)

(-) 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 Q8UVX5_LITPI | Q8UVX5 from UniProtKB/TrEMBL  Length:127

    Alignment length:104
                                    33        43        53        63        73        83        93       103       113       123    
         Q8UVX5_LITPI    24 QDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 127
               SCOP domains d3hg6a_ A: Amphibian cytotoxic ribonuclease                                                              SCOP domains
               CATH domains -3hg6A00 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 -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3hg6 A   1 xDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 104
                            |       10        20        30        40        50        60        70        80        90       100    
                            |                                                                                                       
                            1-PCA                                                                                                   


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 d3hg6a_ A: Amphibian cytotoxic ribonuclease                                                              SCOP domains
               CATH domains -3hg6A00 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
                 3hg6 A   1 xDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 104
                            |       10        20        30        40        50        60        70        80        90       100    
                            1-PCA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3HG6)

(-) Gene Ontology  (5, 10)

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.

Chain A   (Q8UVX5_LITPI | Q8UVX5)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RNP30_LITPI | P22069: 1onc 1pu3 1yv4 1yv6 1yv7 2gmk 2i5s 2kb6 2lt5 3fd7 3phn 3snf 3u00 3u01

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3HG6)