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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
 
Authors :  R. K. Arni, L. Watanabe, R. J. Ward, R. J. Kreitman, K. Kumar, F. G. Walz J
Date :  27 Nov 98  (Deposition) - 25 Mar 99  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D,E  (1x)
Keywords :  Hydrolase, Endoribonuclease, Hydrolase/Rna, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. K. Arni, L. Watanabe, R. J. Ward, R. J. Kreitman, K. Kumar, F. G. Walz Jr.
Three-Dimensional Structure Of Ribonuclease T1 Complexed With An Isosteric Phosphonate Substrate Analogue Of Gpu: Alternate Substrate Binding Modes And Catalysis.
Biochemistry V. 38 2452 1999
PubMed-ID: 10029539  |  Reference-DOI: 10.1021/BI982612Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*GP*(U34))-3'
    ChainsC, D, E
    EngineeredYES
    SyntheticYES
 
Molecule 2 - RIBONUCLEASE T1
    ChainsA, B
    EC Number3.1.27.3
    MutationYES
    Organism ScientificASPERGILLUS ORYZAE
    Organism Taxid5062
    Other DetailsRNASE T1 COMPLEXED WITH 5'-R(*GP*(CH2)U)-3

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A C  
Biological Unit 2 (1x) B DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1U343Mod. NucleotideURIDINE 5'-MONOMETHYLPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1U341Mod. NucleotideURIDINE 5'-MONOMETHYLPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1U342Mod. NucleotideURIDINE 5'-MONOMETHYLPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1B2M)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:2 -A:10
2A:6 -A:103
3B:2 -B:10
4B:6 -B:103

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:38 -Pro A:39
2Ser A:54 -Pro A:55
3Tyr B:38 -Pro B:39
4Ser B:54 -Pro B:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B2M)

(-) Exons   (0, 0)

(no "Exon" information available for 1B2M)

(-) 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:104
 aligned with RNT1_ASPOR | P00651 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:104
                                    36        46        56        66        76        86        96       106       116       126    
           RNT1_ASPOR    27 ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 130
               SCOP domains d1b2ma_ A: RNase T1                                                                                      SCOP domains
               CATH domains 1b2mA00 A:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.hhhhhhhhhhhhhhhh...........eee.............eeeee...............eeeeee....eeeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1b2m A   1 ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with RNT1_ASPOR | P00651 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:104
                                    36        46        56        66        76        86        96       106       116       126    
           RNT1_ASPOR    27 ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 130
               SCOP domains d1b2mb_ B: RNase T1                                                                                      SCOP domains
               CATH domains 1b2mB00 B:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.hhhhhhhhhhhhhhhhh..........eee.............eeeee...............eeeeee....eeeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1b2m B   1 ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    

Chain C from PDB  Type:RNA  Length:2
                                  
                 1b2m C 105 Gu 106
                             |
                           106-U34

Chain D from PDB  Type:RNA  Length:2
                                  
                 1b2m D 105 Gu 106
                             |
                             |
                           106-U34

Chain E from PDB  Type:RNA  Length:2
                                  
                 1b2m E 105 Gu 106
                             |
                             |
                           106-U34

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B2M)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RNT1_ASPOR | P00651)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0046589    ribonuclease T1 activity    Catalysis of the endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Gp with 2',3'-cyclic phosphate intermediates.
    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:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0008150    biological_process    A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0030428    cell septum    A structure composed of peptidoglycan and often chitin in addition to other materials. It usually forms perpendicular to the long axis of a cell or hypha and grows centripetally from the cell wall to the center of the cell and often functions in the compartmentalization of a cell into two daughter cells.
    GO:0001411    hyphal tip    The end, or tip, of a fungal hypha, where polarized growth occurs during hyphal elongation.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNT1_ASPOR | P006511bir 1bu4 1bvi 1ch0 1det 1fys 1fzu 1g02 1gsp 1hyf 1hz1 1i0v 1i0x 1i2e 1i2f 1i2g 1i3f 1i3i 1iyy 1lov 1low 1loy 1lra 1q9e 1rga 1rgc 1rgk 1rgl 1rhl 1rls 1rn1 1rn4 1rnt 1trp 1trq 1tto 1ygw 2aad 2aae 2bir 2bu4 2gsp 2hoh 2rnt 3bir 3bu4 3gsp 3hoh 3rnt 3syu 3urp 4bir 4bu4 4gsp 4hoh 4odk 4rnt 5bir 5bu4 5gsp 5hoh 5rnt 6gsp 6rnt 7gsp 7rnt 8rnt 9rnt

(-) Related Entries Specified in the PDB File

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