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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS MAZF IN COMPLEX WITH RNA
 
Authors :  D. K. Simanshu, D. J. Patel
Date :  23 Aug 13  (Deposition) - 23 Oct 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Toxin-Antitoxin Complex, Toxin-Mrna Complex, Mazf, Mrna Interferase, Endoa, Ydce, Toxin, Antitoxin, Maze, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Simanshu, Y. Yamaguchi, J. H. Park, M. Inouye, D. J. Patel
Structural Basis Of Mrna Recognition And Cleavage By Toxin Mazf And Its Regulation By Antitoxin Maze In Bacillus Subtilis.
Mol. Cell V. 52 447 2013
PubMed-ID: 24120662  |  Reference-DOI: 10.1016/J.MOLCEL.2013.09.006

(-) Compounds

Molecule 1 - MRNA INTERFERASE ENDOA
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BSU04660, MAZF, NDOA, YDCE
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: ENDORIBONUCLEASE ENDOA, TOXIN ENDOA, MRNA INTERFERASE MAZF- BS, MAZF-BS
 
Molecule 2 - RNA, MRNA
    Chains: C
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED SSRNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1DU1Mod. Residue
2IOD6Ligand/IonIODIDE ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:97BINDING SITE FOR RESIDUE IOD A 201
2AC2SOFTWAREGLU A:70 , U C:1BINDING SITE FOR RESIDUE IOD A 202
3AC3SOFTWAREASP A:33 , LYS B:4 , HOH B:435BINDING SITE FOR RESIDUE IOD A 203
4AC4SOFTWAREGLN A:86 , LEU A:88 , HOH A:309 , HOH A:338 , HOH A:355 , HOH A:428BINDING SITE FOR RESIDUE NA A 204
5AC5SOFTWARELYS A:4 , HOH B:302BINDING SITE FOR RESIDUE IOD B 202
6AC6SOFTWAREA C:4BINDING SITE FOR RESIDUE IOD C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MDX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:14 -Pro A:15
2Ser B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MDX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MDX)

(-) Exons   (0, 0)

(no "Exon" information available for 4MDX)

(-) 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    
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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:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...........eeeeee..hhhhhhhh.eeeeeeee..........eeeehhhhhh....eeeeeeeeeeee...eeeeeee.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdx A   0 SMIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...........eeeeee..hhhhhhhh.eeeeeeee..........eeeehhhhhh....eeeeeeeeeeee...eeeeeee.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdx B   0 SMIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain C from PDB  Type:DNA/RNA  Length:9
                                         
                 4mdx C   1 UUxACAUAA   9
                              |      
                              3-DU
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4MDX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MDX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MDX)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  ENDOA_BACSU | P96622
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENDOA_BACSU | P96622: 1ne8 4me7

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