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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE T IN COMPLEX WITH A PREFERRED SSDNA (TAGG) WITH TWO 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 :  2.11
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 :  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, C, D
    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
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: JM109 / ATCC 53323
    Synonym: RNASE T, EXORIBONUCLEASE T
 
Molecule 2 - 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
    Chains: E, F, G, H
    Engineered: YES
    Other Details: SSDNA
    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 , ASP A:186 , DG E:7 , MG E:8BINDING SITE FOR RESIDUE MG A 216
2AC2SOFTWAREASP B:23 , GLU B:25 , ASP B:186 , DG F:7 , MG F:8BINDING SITE FOR RESIDUE MG B 216
3AC3SOFTWAREASP C:23 , GLU C:25 , ASP C:186 , DG G:7 , MG G:8BINDING SITE FOR RESIDUE MG C 216
4AC4SOFTWAREASP D:23 , GLU D:25 , ASP D:186 , DG H:7 , MG H:8BINDING SITE FOR RESIDUE MG D 216
5AC5SOFTWAREASP A:23 , MG A:216 , HOH A:225 , HOH A:336 , DG E:6 , DG E:7 , HOH E:131BINDING SITE FOR RESIDUE MG E 8
6AC6SOFTWAREASP B:23 , MG B:216 , HOH B:230 , HOH B:271 , DG F:6 , DG F:7 , HOH F:308BINDING SITE FOR RESIDUE MG F 8
7AC7SOFTWAREASP C:23 , MG C:216 , HOH C:232 , HOH C:235 , HOH C:279 , DG G:6 , DG G:7BINDING SITE FOR RESIDUE MG G 8
8AC8SOFTWAREASP D:23 , MG D:216 , HOH D:224 , HOH D:226 , HOH D:276 , DG H:6 , DG H:7BINDING SITE FOR RESIDUE MG H 8

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NH1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:207 -Pro A:208
2Trp B:207 -Pro B:208
3Trp C:207 -Pro C:208
4Trp D:207 -Pro D:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NH1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NH1)

(-) Exons   (0, 0)

(no "Exon" information available for 3NH1)

(-) 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:209
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:209
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
            RNT_ECOLI     4 NAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
               SCOP domains d3nh1a_ A: automated matches                                                                                                                                                                                      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
                 3nh1 A   4 NAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:209
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
            RNT_ECOLI     4 NAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
               SCOP domains d3nh1b_ B: automated matches                                                                                                                                                                                      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
                 3nh1 B   4 NAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         


Chain C 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 d3nh1c_ C: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nh1 C   9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
                                    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:205
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:205
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     
            RNT_ECOLI     9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAE 213
               SCOP domains d3nh1d_ D: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------RNase_T-3nh1D01 D:20-194                                                                                                                                                       ------------------- Pfam domains (1)
           Pfam domains (2) -----------RNase_T-3nh1D02 D:20-194                                                                                                                                                       ------------------- Pfam domains (2)
           Pfam domains (3) -----------RNase_T-3nh1D03 D:20-194                                                                                                                                                       ------------------- Pfam domains (3)
           Pfam domains (4) -----------RNase_T-3nh1D04 D:20-194                                                                                                                                                       ------------------- Pfam domains (4)
         Sec.struct. author hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nh1 D   9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAE 213
                                    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
                                    
                 3nh1 E   4 TAGG   7


Chain F from PDB  Type:DNA  Length:5
                                     
                 3nh1 F   3 ATAGG   7


Chain G from PDB  Type:DNA  Length:3
                                   
                 3nh1 G   5 AGG   7


Chain H from PDB  Type:DNA  Length:3
                                   
                 3nh1 H   5 AGG   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NH1)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: RNase_H (288)

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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