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(-) Description

Title :  STRUCTURE OF BINASE MUTANT HIS 101 ASN
 
Authors :  W. A. Offen, A. L. Okorokov
Date :  12 Nov 96  (Deposition) - 12 Mar 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endoribonuclease, Microbial Extracellular Ribonuclease, Phosphodiester Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Okorokov, K. I. Panov, W. A. Offen, V. G. Mukhortov, A. A. Antson, M. Y. A. Karpeisky, A. J. Wilkinson, G. G. Dodson
Rna Cleavage Without Hydrolysis. Splitting The Catalytic Activities Of Binase With Asn101 And Thr101 Mutations.
Protein Eng. V. 10 273 1997
PubMed-ID: 9153077  |  Reference-DOI: 10.1093/PROTEIN/10.3.273
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.27.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PHOA-BINASE HIS101ASN
    Expression System Plasmid: PEXBINN101
    Expression System Strain: EPICURIAN COLI STRAIN XL-1 BLUE MRF'
    Expression System Taxid: 562
    Expression System Vector: PBIT36
    Expression System Vector Type: PR LAMDA PHAGE PROMOTER UNDER CI-TS REGULATION
    Gene: PHOA-BINASE HIS101ASN
    Mutation: YES
    Organism Scientific: BACILLUS INTERMEDIUS
    Organism Taxid: 1400
    Other Details: BINASE GENE CO-EXPRESSED AS FUSION PROTEIN WITH ALKALINE PHOSPHATASE TO ENABLE EXPORT INTO PERIPLASMIC SPACE
    Strain: 7P
    Synonym: BINASE, EXTRACELLULAR RIBONUCLEASE FROM BACILLUS INTERMEDIUS

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2RBI)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
11UNKNOWNLYS A:26 , GLU A:72 , ARG A:86CATALYTIC SITE RESIDUES.
22UNKNOWNASN A:101MUTATED CATALYTIC SITE RESIDUE.
33UNKNOWNGLU A:59MAIN NUCLEOTIDE BINDING RESIDUE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RBI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RBI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RBI)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2RBI)

(-) 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 d2rbia_ A: Binase                                                                                            SCOP domains
               CATH domains 2rbiA00 A:2-109  [code=3.10.450.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.........hhhhhhh........hhhh.........................eeeee...........eeeee....eeee......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2rbi A   2 VINTFDGVADYLIRYKRLPDNYITKSQASALGWVASKGNLAEVAPGKSIGGDVFSNREGRLPSASGRTWREADINYVSGFRNADRLVYSSDWLIYKTTDNYATFTRIR 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 d2rbib_ B: Binase                                                                                            SCOP domains
               CATH domains 2rbiB00 B:2-109  [code=3.10.450.30, no name defined]                                                         CATH domains
           Pfam domains (1) -----------------Ribonuclease-2rbiB01 B:19-108                                                             - Pfam domains (1)
           Pfam domains (2) -----------------Ribonuclease-2rbiB02 B:19-108                                                             - Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhh.........hhhhhhh........hhhh......eeeee..............eeeee...........eeeee....eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2rbi B   2 VINTFDGVADYLIRYKRLPDNYITKSQASALGWVASKGNLAEVAPGKSIGGDVFSNREGRLPSASGRTWREADINYVSGFRNADRLVYSSDWLIYKTTDNYATFTRIR 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  (1, 2)

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

(-) 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

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        RN_BACIN | P00649: 1buj 1gou 1gov 1goy 4haa

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