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(-) Description

Title :  X-RAY-CRYSTALLOGRAPHIC STRUCTURE OF AN RNASE PO1 EXHIBITING ANTI-TUMOR ACTIVITY
 
Authors :  H. Kobayashi, T. Katsurtani, Y. Hara, N. Motoyoshi, T. Itagaki, F. Akit A. Higashiura, Y. Yamada, M. Suzuki, N. Inokuchi
Date :  30 Aug 13  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rnase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kobayashi, T. Katsutani, Y. Hara, N. Motoyoshi, T. Itagaki, F. Akita, A. Higashiura, Y. Yamada, N. Inokuchi, M. Suzuki
X-Ray Crystallographic Structure Of Rnase Po1 That Exhibits Anti-Tumor Activity
Biol. Pharm. Bull. V. 37 968 2014
PubMed-ID: 24882409

(-) Compounds

Molecule 1 - GUANYL-SPECIFIC RIBONUCLEASE PO1
    Chains: A, B, C
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: OYSTER MUSHROOM
    Organism Scientific: PLEUROTUS OSTREATUS
    Organism Taxid: 5322
    Synonym: RNASE PO1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WHO)

(-) Sites  (0, 0)

(no "Site" information available for 3WHO)

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:7 -A:84
2A:9 -A:99
3A:48 -A:82
4B:7 -B:84
5B:9 -B:99
6B:48 -B:82
7C:7 -C:84
8C:9 -C:99
9C:48 -C:82

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:34 -Pro A:35
2Pro A:50 -Thr A:51
3Tyr B:34 -Pro B:35
4Pro B:50 -Thr B:51
5Tyr C:34 -Pro C:35
6Pro C:50 -Thr C:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WHO)

(-) 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:101
 aligned with RNPO_PLEOS | P81762 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           RNPO_PLEOS     1 QTGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPGADRVIYDQSGRFCACLTHTGAPSTNGFVECRF 101
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeehhhhhhhhhhhhhh.......eee.............eeeee..............eeeeee....eeeeee..........ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3who A   1 QTGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPGADRVIYDQSGRFCACLTHTGAPSTNGFVECRF 101
                                    10        20        30        40        50        60        70        80        90       100 


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with RNPO_PLEOS | P81762 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           RNPO_PLEOS     1 QTGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPGADRVIYDQSGRFCACLTHTGAPSTNGFVECRF 101
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeehhhhhhhhhhhhhh.......ee..............eeeee..............eeeeee....eeeeee..........ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3who B   1 QTGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPGADRVIYDQSGRFCACLTHTGAPSTNGFVECRF 101
                                    10        20        30        40        50        60        70        80        90       100 


Chain C from PDB  Type:PROTEIN  Length:101
 aligned with RNPO_PLEOS | P81762 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           RNPO_PLEOS     1 QTGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPGADRVIYDQSGRFCACLTHTGAPSTNGFVECRF 101
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeehhhhhhhhhhhhhh.......eee.............eeeee..............eeeee.....eeeeee..........ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3who C   1 QTGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPGADRVIYDQSGRFCACLTHTGAPSTNGFVECRF 101
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3WHO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RNPO_PLEOS | P81762)
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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  3who
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 Related Entries

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UniProtKB/Swiss-Prot
        RNPO_PLEOS | P81762: 3wr2

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