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(-) Description

Title :  X-RAY STRUCTURE OF THE NON COVALENT SWAPPED FORM OF THE Q28L/K31C/S32C MUTANT OF BOVINE PANCREATIC RIBONUCLEASE IN COMPLEX WITH 2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
 
Authors :  A. Merlino, I. Russo Krauss, M. Perillo, C. A. Mattia, C. Ercole, D. Picone, A. Vergara, F. Sica
Date :  18 Dec 08  (Deposition) - 24 Mar 09  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  3D-Domain Swapping, Bovine Seminal Ribonuclease, Non- Covalent Dimer, Antitumor Activity, Quaternary Structure Flexibility, Protein Mutations And Evolution, Endonuclease, Glycation, Glycoprotein, Hydrolase, Nuclease, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merlino, I. Russo Krauss, M. Perillo, C. A. Mattia, C. Ercole, D. Picone, A. Vergara, F. Sica
Toward An Antitumor Form Of Bovine Pancreatic Ribonuclease: The Crystal Structure Of Three Noncovalent Dimeric Mutants
Biopolymers V. 91 1029 2009
PubMed-ID: 19280639  |  Reference-DOI: 10.1002/BIP.21183
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE PANCREATIC
    Chains: A, B
    EC Number: 3.1.27.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNASE1, RNS1
    Mutation: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: RIBONUCLEASE, RNASE 1, RNASE A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CGP1Ligand/Ion2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
2YCM4Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:41 , VAL A:43 , ASN A:44 , THR A:45 , HIS A:119 , PHE A:120 , HOH A:659 , GLN B:11 , HIS B:12 , HOH B:903BINDING SITE FOR RESIDUE CGP A 900

(-) 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
2Asn A:113 -Pro A:114
3Tyr B:92 -Pro B:93
4Asn B:113 -Pro B:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FL0)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNAS1_BOVIN66-72
 		  2A:40-46
B:40-46

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000115861ENSBTAE00000400684chr10:25757929-2575797345RNAS1_BOVIN-00--
1.2ENSBTAT000000115862ENSBTAE00000093931chr10:25758709-25759510802RNAS1_BOVIN1-1591592A:1-124
B:1-124 (gaps)		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 RNAS1_BOVIN | P61823 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
          RNAS1_BOVIN    27 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 150
               SCOP domains d3fl0a_ A: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains 3fl0A00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.......hhhhhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-124 UniProt: 1-159 [INCOMPLETE]                                                                           Transcript 1
                 3fl0 A   1 KETAAAKFERQHMDSSTSAASSSNYCNLMMccRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM                                                                                        


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with RNAS1_BOVIN | P61823 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
          RNAS1_BOVIN    27 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 150
               SCOP domains d3fl0b_ B: Ribonucl   ease A (also ribonuclease B, S)                                                                        SCOP domains
               CATH domains 3fl0B00 B:1-124 P-3   0 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 1.2  PDB: B:1-124 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                    Transcript 1
                 3fl0 B   1 KETAAAKFERQHMDSSTSA---SNYCNLMMccRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 124
                                    10        |-  |     30||      40        50        60        70        80        90       100       110       120    
                                             19  23      31-YCM                                                                                         
                                                          32-YCM
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FL0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNAS1_BOVIN | P61823)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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
        RNAS1_BOVIN | P61823: 1a2w 1a5p 1a5q 1afk 1afl 1afu 1aqp 1b6v 1bel 1bzq 1c0b 1c0c 1c8w 1c9v 1c9x 1cjq 1cjr 1d5d 1d5e 1d5h 1dfj 1dy5 1eic 1eid 1eie 1eos 1eow 1f0v 1fev 1fs3 1gv7 1izp 1izq 1izr 1j7z 1j80 1j81 1j82 1jn4 1js0 1jvt 1jvu 1jvv 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8 1kh8 1lsq 1o0f 1o0h 1o0m 1o0n 1o0o 1qhc 1rar 1ras 1rat 1rbb 1rbc 1rbd 1rbe 1rbf 1rbg 1rbh 1rbi 1rbj 1rbn 1rbw 1rbx 1rca 1rcn 1rha 1rhb 1rnc 1rnd 1rnm 1rnn 1rno 1rnq 1rnu 1rnv 1rnw 1rnx 1rny 1rnz 1rob 1rpf 1rpg 1rph 1rsm 1rta 1rtb 1ruv 1srn 1ssa 1ssb 1ssc 1u1b 1un5 1w4o 1w4p 1w4q 1wbu 1xps 1xpt 1ymn 1ymr 1ymw 1z3l 1z3m 1z3p 1z6d 1z6s 2aas 2apq 2apu 2blp 2blz 2e33 2e3w 2g4w 2g4x 2g8q 2g8r 2nui 2op2 2oqf 2p42 2p43 2p44 2p45 2p46 2p47 2p48 2p49 2p4a 2qca 2rat 2rln 2rns 2w5g 2w5i 2w5k 2w5l 2w5m 2xog 2xoi 3a1r 3d6o 3d6p 3d6q 3d7b 3d8y 3d8z 3dh5 3dh6 3di7 3di8 3di9 3dib 3dic 3dxg 3dxh 3eux 3euy 3euz 3ev0 3ev1 3ev2 3ev3 3ev4 3ev5 3ev6 3fkz 3fl1 3fl3 3i67 3i6f 3i6h 3i6j 3i7w 3i7x 3i7y 3jw1 3lxo 3mwq 3mwr 3mx8 3mzq 3mzr 3oqy 3oqz 3or0 3ql1 3ql2 3qsk 3rat 3rh1 3rid 3rn3 3rsd 3rsk 3rsp 3srn 4ao1 4g8v 4g8y 4g90 4j5z 4j60 4j61 4j62 4j63 4j64 4j65 4j66 4j67 4j68 4j69 4j6a 4k7l 4k7m 4l55 4mxf 4o36 4o37 4okf 4ooh 4ot4 4peq 4pou 4qh3 4rat 4rsd 4rsk 4rte 4s0q 4s18 4srn 4wyn 4wyp 4wyz 4ygw 4zz4 5d6u 5d97 5e5e 5e5f 5et4 5jlg 5jmg 5jml 5rat 5rsa 6rat 6rsa 7rat 7rsa 8rat 8rsa 9rat 9rsa

(-) Related Entries Specified in the PDB File

1a2w CRYSTAL STRUCTURE OF A 3D DOMAIN-SWAPPED DIMER OF RNASE A
1bsr BOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION
1h8x DOMAIN-SWAPPED DIMER OF A HUMAN PANCREATIC RIBONUCLEASE VARIANT
1tq9 NON-COVALENT SWAPPED DIMER OF BOVINE SEMINAL RIBONUCLEASE IN COMPLEX WITH 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'- MONOPHOSPHATE
3bcp CRYSTAL STRUCTURE OF THE SWAPPED NON COVALENT FORM OF P19A/ L28Q/N67D BS-RNASE
3fkz X-RAY STRUCTURE OF THE NON COVALENT SWAPPED FORM OF THE S16G/T17N/A19P/A20S/K31C/S32C MUTANT OF BOVINE PANCREATIC RIBONUCLEASE
3fl1 X-RAY STRUCTURE OF THE NON COVALENT SWAPPED FORM OF THE A19P/Q28L/K31C/S32C MUTANT OF BOVINE PANCREATIC RIBONUCLEASE IN COMPLEX WITH 2'-DEOXYCYTIDINE-2'- DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
3fl3 X-RAY STRUCTURE OF THE LIGAND FREE NON COVALENT SWAPPED FORM OF THE A19P/Q28L/K31C/S32C MUTANT OF BOVINE PANCREATIC RIBONUCLEASE