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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE SA2
 
Authors :  J. Sevcik, Z. Dauter, K. S. Wilson
Date :  09 Jul 03  (Deposition) - 13 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sevcik, Z. Dauter, K. S. Wilson
Crystal Structure Reveals Two Alternative Conformations In The Active Site Of Ribonuclease Sa2.
Acta Crystallogr. , Sect. D V. 60 1198 2004
PubMed-ID: 15213380  |  Reference-DOI: 10.1107/S0907444904009035
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Strain: R8-26

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:77 , PRO B:14 , SER B:15 , GLN B:16 , PRO B:62 , ARG B:70 , HOH B:244 , HOH B:262BINDING SITE FOR RESIDUE SO4 B 198
2AC2SOFTWAREARG A:34 , GLU A:56 , ARG A:67 , ARG A:71 , HIS A:86 , TYR A:87 , ARG B:42BINDING SITE FOR RESIDUE SO4 A 199
3AC3SOFTWAREARG A:42 , ARG B:34 , GLU B:56 , ARG B:67 , ARG B:71 , HIS B:86 , TYR B:87 , HOH B:277BINDING SITE FOR RESIDUE SO4 B 200
4AC4SOFTWAREPRO A:14 , SER A:15 , GLN A:16 , ARG A:70 , GLN A:91 , HOH A:223 , HOH A:259BINDING SITE FOR RESIDUE SO4 A 201

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:9 -A:97
2B:9 -B:97

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:28 -Pro A:29
2Gly B:28 -Pro B:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PYL)

(-) 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:96
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:96
                                    77        87        97       107       117       127       137       147       157      
         Q53752_STRAU    68 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d1pyla_ A: Ribonuclease Sa2                                                                      SCOP domains
               CATH domains 1pylA00 A:2-97  [code=3.10.450.30, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhhh.........ee................eeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1pyl A   2 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    11        21        31        41        51        61        71        81        91      


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:94
                                    79        89        99       109       119       129       139       149       159    
         Q53752_STRAU    70 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d1pylb_ B: Ribonuclease Sa2                                                                    SCOP domains
               CATH domains 1pylB00 B:4-97  [code=3.10.450.30, no name defined]                                            CATH domains
           Pfam domains (1) ---------Ribonuclease-1pylB01 B:13-93                                                     ---- Pfam domains (1)
           Pfam domains (2) ---------Ribonuclease-1pylB02 B:13-93                                                     ---- Pfam domains (2)
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhhh..........ee................eeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1pyl B   4 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    13        23        33        43        53        63        73        83        93
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q53752_STRAU | Q53752)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q53752_STRAU | Q53752: 1py3 3d4a 3d5g 3d5i 3dgy 3dh2

(-) Related Entries Specified in the PDB File

1lni RIBONUCLEASE SA AT 1.0 A RESOLUTION
1mgr RIBONUCLEASE SA3
1mgw RIBONUCLEASE SA3
1py3 CRYSTAL STRUCTURE OF RIBONUCLEASE SA2
1rgg RIBONUCLEASE SA AT 1.2 A RESOLUTION