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(-) Description

Title :  NON-COVALENT SWAPPED DIMER OF BOVINE SEMINAL RIBONUCLEASE IN COMPLEX WITH 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE
 
Authors :  F. Sica, A. Di Fiore, A. Merlino, L. Mazzarella
Date :  17 Jun 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Dinucleotide Complex, Cytotoxic Action, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Sica, A. Di Fiore, A. Merlino, L. Mazzarella
Structure And Stability Of The Non-Covalent Swapped Dimer Of Bovine Seminal Ribonuclease: An Enzyme Tailored To Evade Ribonuclease Protein Inhibitor
J. Biol. Chem. V. 279 36753 2004
PubMed-ID: 15192098  |  Reference-DOI: 10.1074/JBC.M405655200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE, SEMINAL
    Chains: A, B
    EC Number: 3.1.27.5
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: PANCREATIC TYPE RIBONUCLEASE, SEMINAL RNASE, S- RNASE, RIBONUCLEASE BS-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CPA2Ligand/Ion2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE
2YCM4Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:41 , VAL A:43 , ASN A:44 , THR A:45 , CYS A:65 , GLN A:69 , ASN A:71 , ALA A:109 , HIS A:119 , PHE A:120 , HOH A:202 , LYS B:7 , GLN B:11 , HIS B:12 , ASN B:67 , GLY B:68 , GLN B:69 , HOH B:157BINDING SITE FOR RESIDUE CPA A 126
2AC2SOFTWARELYS A:7 , GLN A:11 , HIS A:12 , ASN A:67 , GLY A:68 , GLN A:69 , LYS B:41 , VAL B:43 , ASN B:44 , THR B:45 , CYS B:65 , GLN B:69 , ASN B:71 , ALA B:109 , HIS B:119 , PHE B:120 , ASP B:121 , HOH B:156 , HOH B:236BINDING SITE FOR RESIDUE CPA B 626

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:84
2A:40 -A:95
3A:58 -A:110
4A:65 -A:72
5B:26 -B:84
6B:40 -B:95
7B:58 -B:110
8B:65 -B:72

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:92 -Pro A:93
2Lys A:113 -Pro A:114
3Tyr B:92 -Pro B:93
4Lys B:113 -Pro B:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TQ9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNS_BOVIN66-72
 		  2A:40-46
B:40-46

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENSBTAT000000362292ENSBTAE00000284222chr10:25625986-2562602439RNS_BOVIN-00--
1.3bENSBTAT000000362293bENSBTAE00000284221chr10:25626721-25627530810RNS_BOVIN1-1591592A:1-124
B:1-124		124
124

(-) 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:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d1tq9a_ A: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 1tq9A00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: A:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 1tq9 A   1 KESAAAKFERQHMDSGNSPSSSSNYCNLMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM                                                                                        


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d1tq9b_ B: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 1tq9B00 B:1-124 P-30 Protein                                                                                                 CATH domains
           Pfam domains (1) RnaseA-1tq9B01 B:1-121                                                                                                   --- Pfam domains (1)
           Pfam domains (2) RnaseA-1tq9B02 B:1-121                                                                                                   --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: B:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 1tq9 B   1 KESAAAKFERQHMDSGNSPSSSSNYCNLMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM
   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RnaseA] (125)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNS_BOVIN | P00669)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0004522    ribonuclease A activity    Catalysis of the endonucleolytic cleavage of RNA to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
biological process
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RNS_BOVIN | P00669: 11ba 11bg 1bsr 1n1x 1n3z 1qwq 1r3m 1r5c 1r5d 1y92 1y94 2lfj 3bcm 3bco 3bcp 3djo 3djp 3djq 3djv 3djx 4n4c

(-) Related Entries Specified in the PDB File

11ba CRYSTAL STRUCTURE OF THE COVALENT SWAPPED DIMER OF THE SAME PROTEIN COMPLEXED WITH URIDYLYL-2',5'-ADENOSINE
11bg COVALENT SWAPPED DIMER OF THE SAME PROTEIN COMPLEXED WITH WITH URIDYLYL-2',5'-GUANOSINE
1bsr CRYSTAL STRUCTURE OF THE COVALENT SWAPPED DIMER OF THE SAME PROTEIN
1n1x CRYSTAL STRUCTURE OF THE MONOMERIC [S- CARBOXYAMIDOMETHYL- CYS31, S-CARBOXYAMIDOMETHYL-CYS32] BOVINE SEMINAL RIBONUCLEASE
1n3z CRYSTAL STRUCTURE OF THE [S-CARBOXYAMIDOMETHYL-CYS31, S- CARBOXYAMIDOMETHYL-CYS32] MONOMERIC DERIVATIVE OF THE BOVINE SEMINAL RIBONUCLEASE IN THE LIGANDED STATE
1r3m CRYSTAL STRUCTURE OF THE DIMERIC UNSWAPPED FORM OF BOVINE SEMINAL RIBONUCLEASE
1r5c COVALENT SWAPPED DIMER OF THE SAME PROTEIN COMPLEXED WITH 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'- MONOPHOSPHATE
1r5d X-RAY STRUCTURE OF BOVINE SEMINAL RIBONUCLEASE SWAPPING DIMER FROM A NEW CRYSTAL FORM