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(-) Description

Title :  CATALYSIS AND 5' END SENSING BY RIBONUCLEASE RNASE J OF THE METALLO-BETA-LACTAMASE FAMILY
 
Authors :  X. Y. Pei, P. Bralley, G. H. Jones, B. F. Luisi
Date :  23 Apr 15  (Deposition) - 19 Aug 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,E,F
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Keywords :  Hydrolase-Rna Complex, Endonuclease, Exonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Y. Pei, P. Bralley, G. H. Jones, B. F. Luisi
Linkage Of Catalysis And 5' End Recognition In Ribonuclease Rnase J
Nucleic Acids Res. V. 43 8066 2015
PubMed-ID: 26253740  |  Reference-DOI: 10.1093/NAR/GKV732

(-) Compounds

Molecule 1 - RIBONUCLEASE J
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2 PLYSS
    Expression System Vector Type: PLASMID
    Fragment: BETA-LACTAMASE DOMAIN AND BETA-CASP DOMAIN, RESIDUES 1-561
    Organism Scientific: STREPTOMYCES COELICOLOR A3(2)
    Organism Taxid: 100226
 
Molecule 2 - 5'-R(*CP*GP*CP*CP*UP*CP)-3'
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2 PLYSS
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES COELICOLOR A3(2)
    Organism Taxid: 100226

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABEF
Biological Unit 1 (1x): A E 
Biological Unit 2 (1x):  B F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1C5P-1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:30 , THR B:207 , SER B:341 , ILE B:343 , PRO B:344 , HIS B:373 , SER B:375 , GLY B:376 , HIS B:377 , ARG B:403 , HIS B:404 , C F:0 , G F:1BINDING SITE FOR RESIDUE C5P B1458
2AC2SOFTWAREHIS B:84 , HIS B:86 , HIS B:151 , ASP B:173 , ZN B:1454 , G F:1BINDING SITE FOR RESIDUE ZN B1453
3AC3SOFTWAREASP B:88 , HIS B:89 , ASP B:173 , HIS B:399 , ZN B:1453 , G F:1BINDING SITE FOR RESIDUE ZN B1454
4AC4SOFTWAREASP A:88 , HIS A:89 , ASP A:173 , HIS A:399 , ZN A:1457 , G E:1BINDING SITE FOR RESIDUE ZN A1456
5AC5SOFTWAREHIS A:84 , HIS A:86 , HIS A:151 , ASP A:173 , ZN A:1456 , G E:1BINDING SITE FOR RESIDUE ZN A1457

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A0V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:55 -Glu A:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A0V)

(-) Exons   (0, 0)

(no "Exon" information available for 5A0V)

(-) 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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee........eeeeee..eeeeeee.............eee..hhhhhhhhh.eeeeee...hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhh.....eee.....eeee..eeeeeeee......eeeeeeee..eeeee................hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhh...........hhhhhhhhhhh.eeeee........hhhhhhhh...........eeee.......hhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh..hhhh.......eeeeee..eeeeeee.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0v A   2 SHPHPELGRPPALPKGGLRVTPLGGLGEIGRNMTVFEYGGRLLIVDCGVLFPEEEQPGIDLILPDFTSIRDRLDDIEGIVLTHGHEDHIGGVPFLLREKPDIPLIGSKLTLALIEAKLQEHRIRPYTLEVAEGHRERVGPFDCEFVAVNHSIPDALAVAIRTPAGMVVHTGDFKMDQLPLDGRLTDLHAFARLSEEGIDLLLADSTNAEVPGFVPPERDISNVLRQVFANARKRIIVASFASHVHRIQQILDAAHEYGRRVAFVGRSMVRNMGIARDLGYLKVPPGLVVDVKTLDDLPDSEVVLVCTGSQGEPMAALSRMANRDHQIRIVNGDTVILASSLIPGNENAVYRVINGLTRWGANVVHKGNAKVHVSGHASAGELLYFYNICRPKNLMPVHGEWRHLRANAELGALTGVPHDRIVIAEDGVVVDLVEGKAKITGKVQAGYVYVDGLS 455
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451    


Chain B from PDB  Type:PROTEIN  Length:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee........eeeeee..eeeeeee.............eee..hhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhh....eee.....eeee..eeeeeee........eeeeeee..eeeee................hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.............hhhhhhhhh.eeeee........hhhhhhhh...........eeee.......hhhhhhhhhhhhhhh..eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh..hhhh.......eeeeee..eeeeeee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0v B   2 SHPHPELGRPPALPKGGLRVTPLGGLGEIGRNMTVFEYGGRLLIVDCGVLFPEEEQPGIDLILPDFTSIRDRLDDIEGIVLTHGHEDHIGGVPFLLREKPDIPLIGSKLTLALIEAKLQEHRIRPYTLEVAEGHRERVGPFDCEFVAVNHSIPDALAVAIRTPAGMVVHTGDFKMDQLPLDGRLTDLHAFARLSEEGIDLLLADSTNAEVPGFVPPERDISNVLRQVFANARKRIIVASFASHVHRIQQILDAAHEYGRRVAFVGRSMVRNMGIARDLGYLKVPPGLVVDVKTLDDLPDSEVVLVCTGSQGEPMAALSRMANRDHQIRIVNGDTVILASSLIPGNENAVYRVINGLTRWGANVVHKGNAKVHVSGHASAGELLYFYNICRPKNLMPVHGEWRHLRANAELGALTGVPHDRIVIAEDGVVVDLVEGKAKITGKVQAGYVYVD 452
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451 


Chain E from PDB  Type:DNA/RNA  Length:6
                                      
                 5a0v E   0 CGCCUC   5


Chain F from PDB  Type:DNA/RNA  Length:6
                                      
                 5a0v F   0 CGCCUC   5
   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  (0, 0)

(no "SCOP Domain" information available for 5A0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A0V)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  5a0v
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 Related Entries

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        O86842_STRCO | O86842: 5a0t

(-) Related Entries Specified in the PDB File

5a0t CATALYSIS AND 5' END SENSING BY RIBONUCLEASE RNASE J OF THE METALLO-BETA-LACTAMASE FAMILY