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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE T IN COMPLEX WITH A DUPLEX DNA PRODUCT (STEM LOOP DNA WITH 2 NUCLEOTIDE 3' OVERHANG)
 
Authors :  Y. -Y. Hsiao, H. S. Yuan
Date :  28 Dec 11  (Deposition) - 11 Jul 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dedd Nucleases Family, Exo-Nuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -Y. Hsiao, Y. Duh, Y. P. Chen, Y. T. Wang, H. S. Yuan
How An Exonuclease Decides Where To Stop In Trimming Of Nucleic Acids: Crystal Structures Of Rnase T-Product Complexes
Nucleic Acids Res. V. 40 8144 2012
PubMed-ID: 22718982  |  Reference-DOI: 10.1093/NAR/GKS548

(-) Compounds

Molecule 1 - RIBONUCLEASE T
    Chains: A, B
    EC Number: 3.1.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: EXORIBONUCLEASE T, RNASE T
 
Molecule 2 - DNA (5'- D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:92 , HOH A:402BINDING SITE FOR RESIDUE CO A 301
2AC2SOFTWAREGLY B:92 , ARG B:135BINDING SITE FOR RESIDUE CO B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VA3)

(-) 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 3VA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VA3)

(-) Exons   (0, 0)

(no "Exon" information available for 3VA3)

(-) 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:205
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:205
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
            RNT_ECOLI     6 QLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLS 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeee.......hhhhhhhhh....hhhhh.eehhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3va3 A   6 QLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLS 210
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:205
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207     
            RNT_ECOLI     8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeee........hhhhhhhhh....hhhh.eehhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhh...hhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3va3 B   8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
                                    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:12
                                            
                 3va3 C   1 GGCCCTGGCCTT  18
                                 || 16  
                                 6|     
                                 13     


Chain D from PDB  Type:DNA  Length:4
                                    
                 3va3 D  15 CCTT  18
   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 3VA3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VA3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VA3)

(-) 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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  3.1.13.-
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3ngy 3ngz 3nh0 3nh1 3nh2 3v9s 3v9u 3v9w 3v9x 3v9z 3va0