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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS COMPLEXED WITH 5'-UMP
 
Authors :  A. Suzuki, T. Numata, M. Yao, M. Kimura, I. Tanaka
Date :  10 Apr 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Plus Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Suzuki, T. Numata, M. Yao, M. Kimura, I. Tanaka
Structure Of Rnase Mc1 From Bitter Gourd Seeds In Complex With 5'Ump
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE MC
    Chains: A
    EC Number: 3.1.27.1
    Organism Common: BALSAM PEAR
    Organism Scientific: MOMORDICA CHARANTIA
    Organism Taxid: 3673
    Synonym: RIBONUCLEASE MC1
    Tissue: SEED

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE
2URA1Ligand/IonURACIL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN 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:227 , HOH A:260 , HOH A:263 , HOH A:286 , HOH A:309 , HOH A:337 , HOH A:386 , HOH A:426BINDING SITE FOR RESIDUE U5P A 500
2AC2SOFTWARETRP A:5 , TRP A:37 , GLN A:39 , GLY A:42 , SER A:44 , HOH A:313 , HOH A:412BINDING SITE FOR RESIDUE URA A 501

(-) 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 1UCD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1UCD)

(-) 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:190
 aligned with RNMC_MOMCH | P23540 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           RNMC_MOMCH     1 FDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQGSGTSLTNCPQGSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 191
               SCOP domains d1ucda_ A: Ribonuclease MC1                                                                                                                                                                     SCOP domains
               CATH domains 1ucdA00 A:1-190 Ribonuclease Rh; Chain A                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhh.....hhhhhh...eeeeeeeee..ee.....-....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeehhhhhhhhhhhhh...eeeeee......eeeeeeeeeee.....ee.........eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RNASE_T2------------------------------------------RNASE_T2_2  --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ucd A   1 FDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQQSGTSLTNCP-GSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 190
                                    10        20        30        40        |-|       59        69        79        89        99       109       119       129       139       149       159       169       179       189 
                                                                           49 |                                                                                                                                            
                                                                             50
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        RNMC_MOMCH | P23540: 1bk7 1j1f 1j1g 1uca 1ucc 1ucg 1v9h

(-) Related Entries Specified in the PDB File

1bk7 SUBSTRATE-FREE FORM
1uca THE SAME ENZYME IS COMPLEXED WITH 2'-UMP
1ucc THE SAME ENZYME IS COMPLEXED WITH 3'-UMP