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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE MONOMERIC [S-CARBOXYAMIDOMETHYL-CYS31, S-CARBOXYAMIDOMETHYL-CYS32] BOVINE SEMINAL RIBONUCLEASE
 
Authors :  F. Sica, A. Di Fiore, A. Zagari, L. Mazzarella
Date :  21 Oct 02  (Deposition) - 26 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Sica, A. Di Fiore, A. Zagari, L. Mazzarella
The Unswapped Chain Of Bovine Seminal Ribonuclease: Crystal Structure Of The Free And Liganded Monomeric Derivative
Proteins V. 52 263 2003
PubMed-ID: 12833549  |  Reference-DOI: 10.1002/PROT.10407
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE, SEMINAL
    ChainsA
    EC Number3.1.27.5
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    Other DetailsSEMINAL FLUID
    SynonymSEMINAL RNASE, RIBONUCLEASE BS-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 1N1X)

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1X)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENSBTAT000000362292ENSBTAE00000284222chr10:25625986-2562602439RNS_BOVIN-00--
1.3bENSBTAT000000362293bENSBTAE00000284221chr10:25626721-25627530810RNS_BOVIN1-1591591A:1-124 (gaps)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:119
 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 d1n1xa_ A: Semin     al ribonucleasease                                                                                      SCOP domains
               CATH domains 1n1xA00 A:1-124      P-30 Protein                                                                                            CATH domains
               Pfam domains RnaseA-1n1xA01 A     :1-121                                                                                              --- 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 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                   Transcript 1
                 1n1x A   1 KESAAAKFERQHMDSG-----SSNYCNLMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10     |   - |      30||      40        50        60        70        80        90       100       110       120    
                                          16    22       31-YCM                                                                                         
                                                          32-YCM                                                                                        

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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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 | P0066911ba 11bg 1bsr 1n3z 1qwq 1r3m 1r5c 1r5d 1tq9 1y92 1y94 2lfj 3bcm 3bco 3bcp 3djo 3djp 3djq 3djv 3djx 4n4c

(-) Related Entries Specified in the PDB File

1bsr THE SWAPPED ISOMER OF THE DIMERIC BOVINE SEMINAL RIBONUCLEASE