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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RNASE MC1 MUTANT Y101A IN COMPLEX WITH 5'-UMP
 
Authors :  K. Kimura, T. Numata, Y. Kakuta, M. Kimura
Date :  26 Jan 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydolase, Nucleic Acid, Rna, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kimura, T. Numata, Y. Kakuta, M. Kimura
Amino Acids Conserved At The C-Terminal Half Of The Ribonuclease T2 Family Contribute To Protein Stability Of The Enzymes
Biosci. Biotechnol. Biochem. V. 68 1748 2004
PubMed-ID: 15322360  |  Reference-DOI: 10.1271/BBB.68.1748
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE MC
    Chains: A
    EC Number: 3.1.27.1
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: BALSAM PEAR
    Organism Scientific: MOMORDICA CHARANTIA
    Organism Taxid: 3673
    Synonym: RIBONUCLEASE MC1, RNASE MC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:52 , PHE A:53 , THR A:86 , ARG A:132 , GLY A:185 , ALA A:186 , HOH A:1030 , HOH A:1043 , HOH A:1068BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREGLY A:35 , LEU A:36 , TRP A:69 , GLU A:84 , TRP A:85 , GLY A:89BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASN A:47 , HIS A:83 , LYS A:87 , HOH A:1083BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREGLN A:9 , HIS A:34 , ASN A:71 , VAL A:72 , LEU A:73 , ARG A:74 , PHE A:80 , HIS A:83 , GLU A:84 , LYS A:87 , HIS A:88 , HOH A:1039 , HOH A:1050 , HOH A:1055 , HOH A:1077BINDING SITE FOR RESIDUE U5P A 1001

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:15 -A:23
2A:48 -A:91
3A:151 -A:184
4A:168 -A:179

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V9H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V9H)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_T2_1PS00530 Ribonuclease T2 family histidine active site 1.RNMC_MOMCH31-38  1A:31-38
2RNASE_T2_2PS00531 Ribonuclease T2 family histidine active site 2.RNMC_MOMCH81-92  1A:80-91

(-) Exons   (0, 0)

(no "Exon" information available for 1V9H)

(-) 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:193
 aligned with RNMC_MOMCH | P23540 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:194
                               1                                                                                                                                                                                              
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
           RNMC_MOMCH     - ---FDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQGSGTSLTNCPQGSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 191
               SCOP domains d1v9ha_ A: Ribonuclease MC1                                                                                                                                                                        SCOP domains
               CATH domains 1v9hA00 A:-2-190 Ribonuclease Rh; Chain A                                                                                                                                                          CATH domains
               Pfam domains ---Ribonuclease_T2-1v9hA01 A:1-181                  -                                                                                                                                    --------- Pfam domains
         Sec.struct. author .....eeeeeeehhhhhhhh..............eeeeeeeee..ee.....-....hhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeehhhhhhhhhhhhh...eeeeee......eeeeeeeeeee.....ee.........eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------RNASE_T2------------------------------------------RNASE_T2_2  --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9h A  -2 YVEFDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQQSGTSLTNCP-GSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAAFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVEVVACFAQDGSTLIDCTRDTCGANFIF 190
                                     7        17        27        37        47 | |    56        66        76        86        96       106       116       126       136       146       156       166       176       186    
                                                                              49 |                                                                                                                                            
                                                                                50
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Ribonuclease_T2] (11)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNMC_MOMCH | P23540)
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: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:0033897    ribonuclease T2 activity    Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.
biological process
    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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  1v9h
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  3.1.27.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNMC_MOMCH | P23540: 1bk7 1j1f 1j1g 1uca 1ucc 1ucd 1ucg

(-) Related Entries Specified in the PDB File

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