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(-) Description

Title :  NONPRODUCTIVE AND NOVEL BINDING MODES IN CYTOTOXIC RIBONUCLEASES FROM RANA CATESBEIANA OF TWO CRYSTAL STRUCTURES COMPLEXED WITH (2,5 CPG) AND D(APCPGPA)
 
Authors :  C. -J. Tsai, J. -H. Liu, Y. -D. Liao, L. -Y. Chen, P. -T. Cheng, Y. -J. Sun
Date :  28 Jun 03  (Deposition) - 15 Jul 04  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytotoxic Ribonucleases, Anti-Tumor Activity, Sialic Binding And Nucleotide Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. -J. Tsai, J. -H. Liu, Y. -D. Liao, L. -Y. Chen, P. -T. Cheng, Y. -J. Sun
Nonproductive And Novel Binding Modes In Cytotoxic Ribonucleases From Rana Catesbeiana Of Two Crystal Structures Complexed With C(2, 5 Cpg) And D(Apcpgpa)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RC-RNASE6 RIBONUCLEASE
    Chains: A
    Organ: OOCYTES
    Organism Common: BULL FROG
    Organism Scientific: RANA CATESBEIANA
    Organism Taxid: 8400

 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
1CG21Ligand/IonCYTIDYL-2'-5'-PHOSPHO-GUANOSINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:9 , HIS A:10 , PHE A:98 , CG2 A:1106 , HOH A:2101 , HOH A:2107BINDING SITE FOR RESIDUE SO4 A1107
2AC2SOFTWAREHIS A:10 , ASN A:34 , THR A:35 , LYS A:49 , ASN A:50 , GLN A:67 , ASN A:69 , PHE A:98 , ALA A:99 , GLY A:100 , VAL A:101 , SO4 A:1107 , HOH A:2106BINDING SITE FOR RESIDUE CG2 A1106

(-) 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  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:73 -Pro A:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1OJ1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:105
 aligned with Q9DFY5_LITCT | Q9DFY5 from UniProtKB/TrEMBL  Length:128

    Alignment length:105
                                    33        43        53        63        73        83        93       103       113       123     
         Q9DFY5_LITCT    24 QDWDTFQKKHLTDTKKVKCDVEMKKALFDCKKTNTFIFARPPRVQALCKNIKDNTNVLSRDVFYLPQCNRKKLPCHYRLDGSTNTICLTCMKELPIHFAGVGKCP 128
               SCOP domains d1oj1a_ A: Amphibian cytotoxic ribonuclease                                                               SCOP domains
               CATH domains -1oj1A00 A:2-105 P-30 Protein                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhee.....hhhhhh.........eee.ee.hhhhhhhh.......eeee....ee..eeeeee...eeeee..ee.eeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1oj1 A   1 xDWDTFQKKHLTDTKKVKCDVEMKKALFDCKKTNTFIFARPPRVQALCKNIKNNTNVLSRDVFYLPQCNRKKLPCHYRLDGSTNTICLTCMKELPIHFAGVGKCP 105
                            |       10        20        30        40        50        60        70        80        90       100     
                            |                                                                                                        
                            1-PCA
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  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 1OJ1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9DFY5_LITCT | Q9DFY5)
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

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UniProtKB/TrEMBL
        Q9DFY5_LITCT | Q9DFY5: 1oj8

(-) Related Entries Specified in the PDB File

1oj8 RETRO AND NOVEL BINDING MODES IN CYTOTOXIC RIBONUCLEASES FROM RANA CATESBEIANA OF TWO CRYSTAL STRUCTURES COMPLEXED WITH (2',5'CPG) AND D(APCPGPA)