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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE T IN COMPLEX WITH A PREFERRED SSDNA (AAA) WITH TWO MG IN THE ACTIVE SITE
 
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 :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
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, C, D
    EC Number: 3.1.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: EXORIBONUCLEASE T, RNASE T
 
Molecule 2 - DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
    Chains: E, F, G, H
    Engineered: YES
    Other Details: SYNTHETIC CONSTRUCT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:23 , GLU A:25 , HIS A:181 , ASP A:186 , DA E:7BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREASP B:23 , GLU B:25 , HIS B:181 , ASP B:186 , DA F:7BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWAREASP C:23 , GLU C:25 , ASP C:186 , DA G:7 , MG G:101BINDING SITE FOR RESIDUE MG C 301
4AC4SOFTWAREASP D:23 , GLU D:25 , HIS D:181 , ASP D:186 , DA H:7BINDING SITE FOR RESIDUE MG D 301
5AC5SOFTWAREASP A:23 , HOH A:406 , HOH A:407 , HOH A:410 , DA E:6 , DA E:7BINDING SITE FOR RESIDUE MG E 101
6AC6SOFTWAREASP B:23 , HOH B:402 , HOH B:404 , DA F:6 , DA F:7 , HOH F:201BINDING SITE FOR RESIDUE MG F 101
7AC7SOFTWAREASP C:23 , MG C:301 , HOH C:403 , HOH C:405 , HOH C:408 , DA G:6 , DA G:7BINDING SITE FOR RESIDUE MG G 101
8AC8SOFTWAREASP D:23 , HOH D:406 , HOH D:408 , HOH D:429 , DA H:6 , DA H:7BINDING SITE FOR RESIDUE MG H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V9X)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Trp A:207 -Pro A:208
2Ala B:180 -His B:181
3Trp B:207 -Pro B:208
4Trp C:207 -Pro C:208
5Trp D:207 -Pro D:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V9X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V9X)

(-) Exons   (0, 0)

(no "Exon" information available for 3V9X)

(-) 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:211
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:211
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
            RNT_ECOLI     5 AQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV 215
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v9x A   5 AQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV 215
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213  
            RNT_ECOLI     4 NAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV 215
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v9x B   4 NAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV 215
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213  


Chain C from PDB  Type:PROTEIN  Length:203
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:203
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208   
            RNT_ECOLI     9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSA 211
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v9x C   9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSA 211
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208   


Chain D from PDB  Type:PROTEIN  Length:204
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:204
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
            RNT_ECOLI     9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v9x D   9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    


Chain E from PDB  Type:DNA  Length:4
                                    
                 3v9x E   4 TAAA   7


Chain F from PDB  Type:DNA  Length:3
                                   
                 3v9x F   5 AAA   7


Chain G from PDB  Type:DNA  Length:3
                                   
                 3v9x G   5 AAA   7


Chain H from PDB  Type:DNA  Length:3
                                   
                 3v9x H   5 AAA   7
   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 3V9X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V9X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V9X)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  3v9x
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  RNT_ECOLI | P30014
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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 3v9z 3va0 3va3 4kaz 4kb0 4kb1

(-) Related Entries Specified in the PDB File

3ngy 3ngz 3nh0 3nh1 3nh2 3v9s 3v9u 3v9w 3v9z 3va0 3va3