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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNSWAPPED FORM OF P19A/L28Q/N67D BS-RNASE
 
Authors :  A. Merlino, C. Ercole, D. Picone, E. Pizzo, L. Mazzarella, F. Sica
Date :  13 Nov 07  (Deposition) - 12 Feb 08  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Domain Swapping, Bovine Seminal Ribonuclease, Non Covalent Dimer, Antitumor Activity, Allosteric Enzyme, Endonuclease, Hydrolase, Nuclease, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Merlino, C. Ercole, D. Picone, E. Pizzo, L. Mazzarella, F. Sica
The Buried Diversity Of Bovine Seminal Ribonuclease: Shape And Cytotoxicity Of The Swapped Non-Covalent Form Of The Enzyme
J. Mol. Biol. V. 376 427 2008
PubMed-ID: 18164315  |  Reference-DOI: 10.1016/J.JMB.2007.11.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEMINAL RIBONUCLEASE
    ChainsA, B
    EC Number3.1.27.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-22B(+)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSRN
    MutationYES
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymSEMINAL RNASE, S-RNASE, RIBONUCLEASE BS-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:11 , HIS A:12 , LYS A:41 , HIS A:119 , PHE A:120 , HOH A:236 , HOH A:729BINDING SITE FOR RESIDUE PO4 A 125
2AC2SOFTWAREGLN A:69 , ASN A:71 , HIS A:119 , HOH A:635BINDING SITE FOR RESIDUE PO4 A 127
3AC3SOFTWARELYS A:76 , HIS A:105BINDING SITE FOR RESIDUE PO4 A 128
4AC4SOFTWAREGLN B:11 , HIS B:12 , LYS B:41 , HIS B:119 , PHE B:120 , HOH B:237 , HOH B:634BINDING SITE FOR RESIDUE PO4 B 126

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:26 -A:84
2A:31 -B:32
3A:32 -B:31
4A:40 -A:95
5A:58 -A:110
6A:65 -A:72
7B:26 -B:84
8B:40 -B:95
9B:58 -B:110
10B:65 -B:72

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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 3BCM)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (1, 2)

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

(-) Sequences/Alignments

Asymmetric 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 d3bcma_ A: Semin     al ribonucleasease                                                                                      SCOP domains
               CATH domains 3bcmA00 A:1-124      P-30 Protein                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...-----..hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeee.eeeeee....eeeeeeee. 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
                 3bcm A   1 KESAAAKFERQHMDSG-----SSNYCNQMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10     |   - |      30        40        50        60        70        80        90       100       110       120    
                                          16    22                                                                                                      

Chain B 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 d3bcmb_ B: Semin     al ribonucleasease                                                                                      SCOP domains
               CATH domains 3bcmB00 B: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: B:1-124 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                   Transcript 1
                 3bcm B   1 KESAAAKFERQHMDSG-----SSNYCNQMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10     |   - |      30        40        50        60        70        80        90       100       110       120    
                                          16    22                                                                                                      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BCM)

(-) Gene Ontology  (11, 11)

Asymmetric 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 | P0066911ba 11bg 1bsr 1n1x 1n3z 1qwq 1r3m 1r5c 1r5d 1tq9 1y92 1y94 2lfj 3bco 3bcp 3djo 3djp 3djq 3djv 3djx 4n4c

(-) Related Entries Specified in the PDB File

3bco THE SAME PROTEIN, SWAPPED FORM
3bcp THE SAME PROTEIN, SWAPPED NON COVALENT FORM