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(-) Description

Title :  SOLUTION STRUCTURE OF THE MONOMERIC N67D MUTANT OF BOVINE SEMINAL RIBONUCLEASE
 
Authors :  F. Avitabile, C. Alfano, R. Spadaccini, O. Crescenzi, A. M. D'Ursi, G. D'Alessio, T. Tancredi, D. Picone
Date :  03 Sep 03  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (16x)
Keywords :  Alpha-Beta-Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Avitabile, C. Alfano, R. Spadaccini, O. Crescenzi, A. M. D'Ursi, G. D'Alessio, T. Tancredi, D. Picone
The Swapping Of Terminal Arms In Ribonucleases: Comparison Of The Solution Structure Of Monomeric Bovine Seminal And Pancreatic Ribonucleases
Biochemistry V. 42 8704 2003
PubMed-ID: 12873130  |  Reference-DOI: 10.1021/BI0342517
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A
    EC Number: 3.1.27.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SRN
    Mutation: YES
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: SEMINAL RIBONUCLEASE

 Structural Features

(-) Chains, Units

  
NMR Structure (16x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QWQ)

(-) Sites  (0, 0)

(no "Site" information available for 1QWQ)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:26 -A:84
2A:40 -A:95
3A:58 -A:110
4A:65 -A:72

(-) Cis Peptide Bonds  (2, 32)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16Tyr A:92 -Pro A:93
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16Lys A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNS_BOVIN66-72  1A:40-46

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENSBTAT000000362292ENSBTAE00000284222chr10:25625986-2562602439RNS_BOVIN-00--
1.3bENSBTAT000000362293bENSBTAE00000284221chr10:25626721-25627530810RNS_BOVIN1-1591591A:1-124124

(-) Sequences/Alignments

NMR Structure
   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 d1qwqa_ A: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 1qwqA00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains RnaseA-1qwqA01 A:1-121                                                                                                   --- Pfam domains
         Sec.struct. author ...hhhhhhhhh........hhhhhhhhhhhhhh........eeeee..hhhhhhhhhh.eeee......eeee....eeeeeee............eeeeeeeeeeeeee....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
                 1qwq A   1 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: RnaseA] (125)

(-) Gene Ontology  (11, 11)

NMR Structure(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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  Cis Peptide Bonds
    Lys A:113 - Pro A:114   [ RasMol ]  
    Tyr A:92 - Pro A:93   [ RasMol ]  
 

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  1qwq
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  3.1.27.5
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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 1r3m 1r5c 1r5d 1tq9 1y92 1y94 2lfj 3bcm 3bco 3bcp 3djo 3djp 3djq 3djv 3djx 4n4c

(-) Related Entries Specified in the PDB File

4980 1H AND 15N SEQUENTIAL ASSIGNMENT AND SECONDARY STRUCTURE OF THE SAME PROTEIN
1bsr X-RAY STRUCTURE OF BOVINE SEMINAL RIBONUCLEASE