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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE Z IN COMPLEX WITH PRECURSOR TRNA(THR)
 
Authors :  O. Pellegrini, I. Li De La Sierra-Gallay, J. Piton, L. Gilet, C. Cond
Date :  31 Jul 12  (Deposition) - 31 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Zinc-Dependent Metalo Betalactamase - Rna Complex, Trna Maturase, Protein-Rna Complex, Trna Binding, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Pellegrini, I. Li De La Sierra-Gallay, J. Piton, L. Gilet, C. Condon
Activation Of Trna Maturation By Downstream Uracil Residues In B. Subtilis
Structure V. 20 1769 2012
PubMed-ID: 22940585  |  Reference-DOI: 10.1016/J.STR.2012.08.002

(-) Compounds

Molecule 1 - RIBONUCLEASE Z
    Chains: A
    EC Number: 3.1.26.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: BSU23840, RNZ, YQJK
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: RNASE Z, TRNA 3 ENDONUCLEASE, TRNASE Z
 
Molecule 2 - TRNA(THR)
    Chains: B
    Engineered: YES
    Other Details: B.SUBTILIS TRNATHR(ENCODED BY THE TRN1-THR GENE) WAS SYNTHETISED AS A PRECURSOR WITH 2 NT 3'-EXTENSION. THE NT 73-76 ARE 2'-O-METHYLATED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2OMU2Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2OMU2Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2OMU2Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2OMU4Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:67 , HIS A:68 , ASP A:211 , HIS A:269 , ZN A:402 , OMU B:74BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:63 , HIS A:65 , HIS A:140 , ASP A:211 , ZN A:401 , OMU B:74BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREARG A:54 , ASP A:86 , U B:4BINDING SITE FOR RESIDUE MES A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GCW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4GCW)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.............eeeeeehhhhheeeee....hhhhhhh....hhh.eeeee....hhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhh........eeeee...eeeee...eeeeeeee.....eeeeeeee.......hhhhhhhh.....hhhhhhhhh..ee.....eehhhhhh.......eeee......hhhhhhhh....eeeee......hhhhhhhh...hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhh....eee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gcw A   1 MELLFLGTGAGIPAKARNVTSVALKLLEERRSVWLFDCGEATQHQMLHTTIKPRKIEKIFITHMHGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKTHLTYPLAIQEIEEGIVFEDDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEMNIPPGPVYQKIKKGETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARDCDVMVHEATFAKEDRKLAYDYYHSTTEQAAVTAKEARAKQLILTHISARYQGDASLELQKEAVDVFPNSVAAYDFLEVNVPRG 307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       


Chain B from PDB  Type:RNA  Length:55
                                                                                       
                 4gcw B   1 GCUUCCAUAGCUCAGCAGGUAGAGCAGUCAGCGGUUCGAGCCCGCUUGGAAGCuu  74
                                    10        20     || 49        59        69   ||
                                                    26|                         73-OMU
                                                     46                          74-OMU
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  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 4GCW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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 Related Entries

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        RNZ_BACSU | P54548: 1y44 2fk6

(-) Related Entries Specified in the PDB File

1y44 2fk6