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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE T IN COMPLEX WITH A NON-PREFERRED SSDNA (GC) WITH ONE MG IN THE ACTIVE SITE
 
Authors :  Y. -Y. Hsiao, H. S. Yuan
Date :  14 Jun 10  (Deposition) - 16 Feb 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Exoribonuclease, Rna Processing, Rna Maturation, Protein-Dna Interactions, Protein-Dna Complex, Exo-Nuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -Y. Hsiao, C. -C. Yang, C. L. Lin, J. L. J. Lin, Y. Duh, H. S. Yuan
Structural Basis For Rna Trimming By Rnase T In Stable Rna 3'-End Maturation
Nat. Chem. Biol. V. 7 236 2011
PubMed-ID: 21317904  |  Reference-DOI: 10.1038/NCHEMBIO.524

(-) Compounds

Molecule 1 - RIBONUCLEASE T
    Chains: A, B
    EC Number: 3.1.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNT
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: JM109 / ATCC 53323
    Synonym: RNASE T, EXORIBONUCLEASE T
 
Molecule 2 - 5'-D(P*GP*C)-3'
    Chains: C, D
    Engineered: YES
    Other Details: SSDNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:23 , HOH A:1001 , HOH A:1002 , HOH A:1004 , HOH C:1003 , HOH C:1005BINDING SITE FOR RESIDUE MG A 1000
2AC2SOFTWAREARG A:135 , HOH A:227BINDING SITE FOR RESIDUE CO A 217
3AC3SOFTWAREASP B:23 , HOH B:2002 , HOH B:2003 , HOH B:2005 , HOH D:2001 , HOH D:2004BINDING SITE FOR RESIDUE MG B 2000
4AC4SOFTWAREARG B:135 , HOH B:233BINDING SITE FOR RESIDUE CO B 217

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NGZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:207 -Pro A:208
2Trp B:207 -Pro B:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NGZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NGZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3NGZ)

(-) 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    
   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:207
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       
            RNT_ECOLI     8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEE 214
               SCOP domains d3ngza_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeee........hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngz A   8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEE 214
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:206
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
            RNT_ECOLI     8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAE 213
               SCOP domains d3ngzb_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------RNase_T-3ngzB01 B:20-194                                                                                                                                                       ------------------- Pfam domains (1)
           Pfam domains (2) ------------RNase_T-3ngzB02 B:20-194                                                                                                                                                       ------------------- Pfam domains (2)
         Sec.struct. author .hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhh..hhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngz B   8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAE 213
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      


Chain C from PDB  Type:DNA  Length:2
                                  
                 3ngz C   1 GC   2


Chain D from PDB  Type:DNA  Length:2
                                  
                 3ngz D   1 GC   2
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NGZ)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNT_ECOLI | P30014)
molecular function
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016896    exoribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNT_ECOLI | P30014: 2is3 3ngy 3nh0 3nh1 3nh2 3v9s 3v9u 3v9w 3v9x 3v9z 3va0 3va3 4kaz 4kb0 4kb1

(-) Related Entries Specified in the PDB File

3ngy RNASE T (E92G MUTANT)
3nh0 RNASE T IN COMPLEX WITH A NON-PREFERRED SSDNA (AAC)
3nh1 RNASE T IN COMPLEX WITH A PREFERRED SSDNA (TAGG) WITH TWO MG IN THE ACTIVE SITE
3nh2 RNASE T IN COMPLEX WITH A STEM DNA WITH A 3' OVERHANG