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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE SA2
 
Authors :  J. Sevcik, Z. Dauter, K. S. Wilson
Date :  08 Jul 03  (Deposition) - 13 Jul 04  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (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, C
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:34 , GLU A:56 , ARG A:67 , ARG A:71 , HIS A:86 , TYR A:87 , ARG C:45 , HOH C:180BINDING SITE FOR RESIDUE SO4 A 300

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:9 -A:97
2B:9 -B:97
3C:9 -C:97

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:28 -Pro A:29
2Gly B:28 -Pro B:29
3Gly C:28 -Pro C:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PY3)

(-) Exons   (0, 0)

(no "Exon" information available for 1PY3)

(-) 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: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 d1py3a_ A: Ribonuclease Sa2                                                                    SCOP domains
               CATH domains 1py3A00 A:4-97  [code=3.10.450.30, no name defined]                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhhh..........ee..............eeeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1py3 A   4 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    13        23        33        43        53        63        73        83        93    


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

    Alignment length:97
                                    76        86        96       106       116       126       136       146       156       
         Q53752_STRAU    67 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d1py3b_ B: Ribonuclease Sa2                                                                       SCOP domains
               CATH domains 1py3B00 B:1-97  [code=3.10.450.30, no name defined]                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhhhhhhhhhhh...........................eeee....---.....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1py3 B   1 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTP---DRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    10        20        30        40        50        60 |   |  70        80        90       
                                                                                        62  66                               


Chain C from PDB  Type:PROTEIN  Length:92
 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 d1py3c_ C: Ribonuclease Sa2                                                                      SCOP domains
               CATH domains 1py3C00 C:2-97  [code=3.10.450.30, no name defined]                                              CATH domains
           Pfam domains (1) -----------Ribonuclease-1py3C01 C:13-93                                                     ---- Pfam domains (1)
           Pfam domains (2) -----------Ribonuclease-1py3C02 C:13-93                                                     ---- Pfam domains (2)
           Pfam domains (3) -----------Ribonuclease-1py3C03 C:13-93                                                     ---- Pfam domains (3)
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhh..........eee..............eeeee....----....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1py3 C   2 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTP----RGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    11        21        31        41        51        61|    |  71        81        91      
                                                                                       62   67
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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: 1pyl 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
1rgg RIBONUCLEASE SA AT 1.2 A RESOLUTION