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(-) Description

Title :  RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS
 
Authors :  K. M. Polyakov, A. A. Lebedev, A. G. Pavlovsky, R. G. Sanishvili, G. G. Dodson
Date :  26 Oct 01  (Deposition) - 29 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Endoribonuclease, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Polyakov, A. A. Lebedev, A. L. Okorokov, K. I. Panov, A. A. Schulga, A. G. Pavlovsky, M. Y. A. Karpeisky, G. G. Dodson
The Structure Of Substrate-Free Microbial Ribonuclease Binase And Of Its Complexes With 3'Gmp And Sulfate Ions
Acta Crystallogr. , Sect. D V. 58 744 2002
PubMed-ID: 11976484  |  Reference-DOI: 10.1107/S0907444902003207
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.27.3
    Organism Scientific: BACILLUS INTERMEDIUS
    Organism Taxid: 1400
    Other Details: RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS
    Synonym: BINASE

 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
1AC1SOFTWARELYS A:26 , GLU A:72 , ARG A:82 , ARG A:86 , HIS A:101 , TYR A:102 , HOH A:2086BINDING SITE FOR RESIDUE SO4 A1110
2AC2SOFTWARETRP A:34 , ALA A:36 , SER A:37 , GLY A:39 , PHE A:81 , ARG A:82 , HOH A:2087 , HOH A:2088 , HOH B:2085BINDING SITE FOR RESIDUE SO4 A1111
3AC3SOFTWARELYS B:26 , GLU B:72 , ARG B:82 , ARG B:86 , HIS B:101 , TYR B:102 , HOH B:2092BINDING SITE FOR RESIDUE SO4 B1110
4AC4SOFTWARETRP B:34 , ALA B:36 , GLY B:39 , PHE B:81 , ARG B:82 , HOH B:2093 , HOH B:2094BINDING SITE FOR RESIDUE SO4 B1111

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GOV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GOV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GOV)

(-) 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:108
 aligned with RN_BACIN | P00649 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:108
                                    64        74        84        94       104       114       124       134       144       154        
             RN_BACIN    55 VINTFDGVADYLIRYKRLPDNYITKSQASALGWVASKGNLAEVAPGKSIGGDVFSNREGRLPSASGRTWREADINYVSGFRNADRLVYSSDWLIYKTTDHYATFTRIR 162
               SCOP domains d1gova_ A: Binase                                                                                            SCOP domains
               CATH domains 1govA00 A:2-109  [code=3.10.450.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eehhhhhhhhh......hhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1gov A   2 VINTFDGVADYLIRYKRLPNDYITKSQASALGWVASKGDLAEVAPGKSIGGDVFSNREGRLPSAGSRTWREADINYVSGFRNADRLVYSSDWLIYKTTDHYATFTRIR 109
                                    11        21        31        41        51        61        71        81        91       101        


Chain B from PDB  Type:PROTEIN  Length:108
 aligned with RN_BACIN | P00649 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:108
                                    64        74        84        94       104       114       124       134       144       154        
             RN_BACIN    55 VINTFDGVADYLIRYKRLPDNYITKSQASALGWVASKGNLAEVAPGKSIGGDVFSNREGRLPSASGRTWREADINYVSGFRNADRLVYSSDWLIYKTTDHYATFTRIR 162
               SCOP domains d1govb_ B: Binase                                                                                            SCOP domains
               CATH domains 1govB00 B:2-109  [code=3.10.450.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1gov B   2 VINTFDGVADYLIRYKRLPNDYITKSQASALGWVASKGDLAEVAPGKSIGGDVFSNREGRLPSAGSRTWREADINYVSGFRNADRLVYSSDWLIYKTTDHYATFTRIR 109
                                    11        21        31        41        51        61        71        81        91       101
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GOV)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RN_BACIN | P00649)
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: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
        RN_BACIN | P00649: 1buj 1gou 1goy 2rbi 4haa

(-) Related Entries Specified in the PDB File

1buj STRUCTURE OF BINASE IN SOLUTION
1gou STRUCTURE OF RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) UNLIGANDED FORM
1goy STRUCTURE OF RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH GUANOSINE-3'-PHOSPHATE (3'-GMP)
2rbi STRUCTURE OF BINASE MUTANT HIS 101 ASN