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(-) Description

Title :  RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP
 
Authors :  U. Langhorst, R. Loris, V. P. Denisov, J. Doumen, P. Roose, D. Maes, B. Halle, J. Steyaert
Date :  15 Sep 98  (Deposition) - 23 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Endoribonuclease, Ribonuclease, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Langhorst, R. Loris, V. P. Denisov, J. Doumen, P. Roose, D. Maes, B. Halle, J. Steyaert
Dissection Of The Structural And Functional Role Of A Conserved Hydration Site In Rnase T1.
Protein Sci. V. 8 722 1999
PubMed-ID: 10211818
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (RIBONUCLEASE T1)
    Chains: A, B, C, D
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: WK6
    Expression System Taxid: 562
    Organism Scientific: ASPERGILLUS ORYZAE
    Organism Taxid: 5062
    Other Details: COMPLEXED WITH GUANOSINE-2'-MONOPHOSPHATE
    Synonym: RNASE T1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
12GP5Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2CA2Ligand/IonCALCIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY C:47 , ASP C:49 , HOH C:288 , TYR D:45 , HOH D:277 , HOH D:278BINDING SITE FOR RESIDUE CA C 250
02AC2SOFTWARETYR C:45 , HOH C:283 , GLY D:47 , ASP D:49 , HOH D:307BINDING SITE FOR RESIDUE CA D 251
03AC3SOFTWAREASN A:36 , TYR A:38 , HIS A:40 , LYS A:41 , TYR A:42 , ASN A:43 , ASN A:44 , TYR A:45 , GLU A:46 , GLU A:58 , ASN A:98 , PHE A:100 , HOH A:269 , HOH D:267 , HOH D:322BINDING SITE FOR RESIDUE 2GP A 252
04AC4SOFTWARETYR B:38 , HIS B:40 , LYS B:41 , TYR B:42 , ASN B:43 , ASN B:44 , TYR B:45 , GLU B:46 , GLU B:58 , ASN B:98 , PHE B:100 , HOH B:307 , HOH D:290 , HOH D:314BINDING SITE FOR RESIDUE 2GP B 253
05AC5SOFTWARESER A:53 , HOH A:258 , HOH A:260 , HOH A:262 , HOH A:267 , HIS C:40 , LYS C:41 , TYR C:42 , ASN C:43 , ASN C:44 , TYR C:45 , GLU C:46 , ASN C:99 , PHE C:100 , HOH D:308BINDING SITE FOR RESIDUE 2GP C 254
06AC6SOFTWARESER A:53 , SER A:54 , PRO A:55 , ASN A:81 , GLU A:82 , ASN A:83 , HOH A:258 , HOH A:260 , HOH A:267 , ASN C:36 , TYR C:38 , HIS C:40 , GLU C:58 , SER C:72 , PRO C:73 , GLY C:74 , ARG C:77 , HIS C:92 , ASN C:98 , PHE C:100 , HOH D:279BINDING SITE FOR RESIDUE 2GP C 255
07AC7SOFTWAREHOH B:279 , HOH B:302 , TYR D:38 , HIS D:40 , LYS D:41 , TYR D:42 , ASN D:43 , ASN D:44 , TYR D:45 , GLU D:46 , GLU D:58 , ASN D:98 , PHE D:100BINDING SITE FOR RESIDUE 2GP D 256
08BI1AUTHORTYR A:42 , ASN A:43 , ASN A:44 , TYR A:45 , GLU A:46BINDING SITE.
09BI2AUTHORTYR B:42 , ASN B:43 , ASN B:44 , TYR B:45 , GLU B:46BINDING SITE.
10BI3AUTHORTYR C:42 , ASN C:43 , ASN C:44 , TYR C:45 , GLU C:46BINDING SITE.
11BI4AUTHORTYR D:42 , ASN D:43 , ASN D:44 , TYR D:45 , GLU D:46BINDING SITE.
12CA1AUTHORASP C:49SITE.
13CA2AUTHORASP D:49SITE.
14CT1AUTHORTYR A:38 , HIS A:40 , GLU A:58 , ARG A:77 , HIS A:92ACTIVE SITE.
15CT2AUTHORTYR B:38 , HIS B:40 , GLU B:58 , ARG B:77 , HIS B:92ACTIVE SITE.
16CT3AUTHORTYR C:38 , HIS C:40 , GLU C:58 , ARG C:77 , HIS C:92ACTIVE SITE.
17CT4AUTHORTYR D:38 , HIS D:40 , GLU D:58 , ARG D:77 , HIS D:92ACTIVE SITE.

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:10
2A:6 -A:103
3B:2 -B:10
4B:6 -B:103
5C:2 -C:10
6C:6 -C:103
7D:2 -D:10
8D:6 -D:103

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological 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
5Tyr C:38 -Pro C:39
6Ser C:54 -Pro C:55
7Tyr D:38 -Pro D:39
8Ser D:54 -Pro D:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BVI)

(-) 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: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 d1bvia_ A: RNase T1                                                                                      SCOP domains
               CATH domains 1bviA00 A:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1bvi A   1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 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 d1bvib_ B: RNase T1                                                                                      SCOP domains
               CATH domains 1bviB00 B:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1bvi B   1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain C 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 d1bvic_ C: RNase T1                                                                                      SCOP domains
               CATH domains 1bviC00 C:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1bvi C   1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain D 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 d1bvid_ D: RNase T1                                                                                      SCOP domains
               CATH domains 1bviD00 D:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1bvi D   1 ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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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  1bvi
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNT1_ASPOR | P00651: 1b2m 1bir 1bu4 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

(no "Related Entries Specified in the PDB File" available for 1BVI)