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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE PARN IN COMPLEX WITH M7GPPPG
 
Authors :  M Wu, H Song
Date :  13 May 08  (Deposition) - 17 Mar 09  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Parn, Cap Analogue, Exonuclease, Hydrolase, Magnesium, Metal-Binding, Nonsense-Mediated Mrna Decay, Nuclease, Nucleus, Phosphoprotein, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wu, P. Nilsson, N. Henriksson, A. Niedzwiecka, M. K. Lim, Z. Cheng, K. Kokkoris, A. Virtanen, H. Song
Structural Basis Of M(7)Gpppg Binding To Poly(A)-Specific Ribonuclease.
Structure V. 17 276 2009
PubMed-ID: 19217398  |  Reference-DOI: 10.1016/J.STR.2008.11.012

(-) Compounds

Molecule 1 - POLY(A)-SPECIFIC RIBONUCLEASE PARN
    Chains: A, B
    EC Number: 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL-21
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Fragment: MPARN
    Gene: PARN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: POLYADENYLATE-SPECIFIC RIBONUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
17MG2Mod. Residue7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:319 , ASN A:333 , LYS A:447 , TRP A:449 , LYS A:450 , THR A:451 , TRP A:468 , ASP A:470 , ASP A:471BINDING SITE FOR RESIDUE 7MG A 651
2AC2SOFTWAREPHE A:31 , HIS A:280 , ASN A:281 , LEU A:284 , LYS A:319 , THR A:334 , SER A:335 , LEU A:336 , MET A:418 , ARG A:419 , HOH A:903 , HOH A:906BINDING SITE FOR RESIDUE GDP A 652
3AC3SOFTWARELYS B:447 , TRP B:449 , LYS B:450 , TRP B:468 , ASP B:470 , ASP B:471 , HOH B:1161BINDING SITE FOR RESIDUE 7MG B 1152
4AC4SOFTWAREARG A:99 , ASP B:471BINDING SITE FOR RESIDUE GDP B 1151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D45)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gln A:325 -Pro A:326
2Thr A:346 -Pro A:347
3Gly A:430 -Pro A:431
4Gln B:325 -Pro B:326
5Thr B:346 -Pro B:347

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D45)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D45)

(-) Exons   (0, 0)

(no "Exon" information available for 3D45)

(-) 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:383
 aligned with PARN_MOUSE | Q8VDG3 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:505
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498     
           PARN_MOUSE     - --MEIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPKPFSRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRSQANGAGALAKCPVTIPEDQKKFIDQVIEKIEDFLQSEEKRSLELDPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSLLSPPKMCVSARSKLIEPFFNKLFLMRVMDIPYLNLEGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYA 503
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhhh.eeeeeeee.....--------....hhhhhhhhhhhhhh...eeeeeeeeeee......eeeeeeeee.............eeeeehhhhhhhhh...hhhhhhh......hhhhhhhhhhhh..-----------------------------------------------------------------------------------------------------...hhhhhhhhh.hhhhhhhhhhhh.eeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeehhhhh...hhhhhh...hhhhhhhhh.........eee........----...hhhhhhhhhhhhhhhhhhhhh.---------......hhhhh.ee..........ee........hhh.eeeee.....hhhhhhhhhhhhh..eeee....eeeee..hhhhhhhhhhhhh.....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d45 A 901 GPMEIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISD--------SGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPKPFSRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDE-----------------------------------------------------------------------------------------------------YTKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYD----QLHEAGYDAYITGLCFISMANYLGS---------SARSKLIEPFFNKLFLMRVMDIPYLNLEGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYA 503
                            |||      8        18        28       | -      | 48        58        68        78        88        98       108       118       128       138       148         -         -         -         -         -         -         -         -         -         - |     258       268       278       288       298       308       318       328       338       348       358    |  368       378       388   |     -   |   408       418       428       438       448       458       468       478       488       498     
                            |||                                 36       45                                                                                                    148                                                                                                   250                                                                                                              363  368                     392       402                                                                                                     
                          901||                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                           900|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:373
 aligned with PARN_MOUSE | Q8VDG3 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:507
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       
           PARN_MOUSE     - --MEIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPKPFSRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRSQANGAGALAKCPVTIPEDQKKFIDQVIEKIEDFLQSEEKRSLELDPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSLLSPPKMCVSARSKLIEPFFNKLFLMRVMDIPYLNLEGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYAEY 505
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhhhhhhhhh.eeeeeeee.......hhhhhh....hhhhhhhhhhhhhh...eeeeeeeeeee......eeeeeeeee.............eeeeehhhhhhhhhh..hhhhhhh......hhhhhhhhh.----------------------------------------------------------------------------------------------------------.hhhhhhhhhh.hhhhhhhhhhhh.eeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeehhhhh...hhhhhh...hhhhhhhhh.........eee..------------.hhhhhhhhhhhhhhhhhhhhh-------------...hhhhh.......---.................eeeee.....hhhhhhhhhhhhh..eeeeee..eeeee....hhhhhhhhh.......eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d45 B 901 GPMEIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPKPFSRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLRE----------------------------------------------------------------------------------------------------------TKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFDPPKVESAE------------HEAGYDAYITGLCFISMANYLG-------------SKLIEPFFNKLFLMR---IPYLNLEGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYAEY 505
                            |||      8        18        28        38        48        58        68        78        88        98       108       118       128       138     |   -         -         -         -         -         -         -         -         -         -         -  |    258       268       278       288       298       308       318       328       338       348        |-         - |     378       388  |      -      |408       418|   |  428       438       448       458       468       478       488       498       
                          901||                                                                                                                                            144                                                                                                        251                                                                                                       357          370                  391           405           419 423                                                                                  
                           900|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                              1
   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  (0, 0)

(no "SCOP Domain" information available for 3D45)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D45)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D45)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PARN_MOUSE | Q8VDG3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004535    poly(A)-specific ribonuclease activity    Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3d45
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARN_MOUSE | Q8VDG3: 1ug8 1whv 2rok

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3D45)