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(-) Description

Title :  ASP79 MAKES A LARGE, UNFAVORABLE CONTRIBUTION TO THE STABILITY OF RNASE SA
 
Authors :  S. R. Trevino, K. Gokulan, S. Newsom, R. L. Thurlkill, K. L. Shaw, V. A. Mitkevich, A. A. Makarov, J. C. Sacchettini, J. M. Scholtz, C. N. Pace
Date :  25 Jan 05  (Deposition) - 19 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  X
Keywords :  Conformational Stability, Electrostatic Strain, Pka, Hydrogen Bonds And Ion Pair. , Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Trevino, K. Gokulan, S. Newsom, R. L. Thurlkill, K. L. Shaw, V. A. Mitkevich, A. A. Makarov, J. C. Sacchettini, J. M. Scholtz, C. N. Pace
Asp79 Makes A Large, Unfavorable Contribution To The Stability Of Rnase Sa.
J. Mol. Biol. V. 354 967 2005
PubMed-ID: 16288913  |  Reference-DOI: 10.1016/J.JMB.2005.09.091
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANYL-SPECIFIC RIBONUCLEASE SA
    Chains: X
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH100
    Expression System Strain: MQ
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Synonym: RNASE SA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU X:54 , ARG X:65 , ARG X:69 , HIS X:85 , TYR X:86 , HOH X:204 , HOH X:293BINDING SITE FOR RESIDUE SO4 X 157

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1X:7 -X:96

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly X:26 -Pro X:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YNV)

(-) Exons   (0, 0)

(no "Exon" information available for 1YNV)

(-) 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 X from PDB  Type:PROTEIN  Length:96
 aligned with RNSA_STRAU | P05798 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:96
                                    10        20        30        40        50        60        70        80        90      
            RNSA_STRAU    1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 96
               SCOP domains d1ynvx_ X: automated matches                                                                     SCOP domains
               CATH domains 1ynvX00 X:1-96  [code=3.10.450.30, no name defined]                                              CATH domains
               Pfam domains ----------Ribonuclease-1ynvX01 X:11-92                                                      ---- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhh............................eeee............eeee......eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  1ynv X  1 DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDKTC 96
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Ribonuclease] (57)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (RNSA_STRAU | P05798)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0046589    ribonuclease T1 activity    Catalysis of the endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Gp with 2',3'-cyclic phosphate intermediates.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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
        RNSA_STRAU | P05798: 1ay7 1box 1c54 1gmp 1gmq 1gmr 1i70 1i8v 1lni 1rge 1rgf 1rgg 1rgh 1rsn 1sar 1t2h 1t2i 1uci 1ucj 1uck 1ucl 1zgx 2sar 3a5e 4gho 4j5g 4j5k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YNV)