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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.
 
Authors :  C. D. Lima, L. K. Wang, S. Shuman
Date :  24 Oct 99  (Deposition) - 29 Nov 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Rna Triphosphatase, Beta Subunit, Polynucleotide 5'-Triphosphatase, Mrna Processing, Mrna Capping, Nuclear Protein Beta Barrel, Catalytic Domain, Dimer, Manganese-Sulfate Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Lima, L. K. Wang, S. Shuman
Structure And Mechanism Of Yeast Rna Triphosphatase: An Essential Component Of The Mrna Capping Apparatus.
Cell(Cambridge, Mass. ) V. 99 533 1999
PubMed-ID: 10589681  |  Reference-DOI: 10.1016/S0092-8674(00)81541-X

(-) Compounds

Molecule 1 - MRNA TRIPHOSPHATASE CET1
    Chains: A, B, C
    EC Number: 3.1.3.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:305 , GLU A:307 , GLU A:496 , SO4 A:601 , HOH A:620 , HOH A:767BINDING SITE FOR RESIDUE MN A 550
2AC2SOFTWAREGLU B:305 , GLU B:307 , GLU B:496 , HOH B:618 , HOH B:641 , HOH B:713BINDING SITE FOR RESIDUE MN B 550
3AC3SOFTWAREGLU C:305 , GLU C:307 , GLU C:496 , SO4 C:603 , HOH C:614 , HOH C:763BINDING SITE FOR RESIDUE MN C 550
4AC4SOFTWAREARG A:393 , LYS A:456 , ARG A:458 , MN A:550 , HOH A:779BINDING SITE FOR RESIDUE SO4 A 601
5AC5SOFTWAREASP B:377 , ARG B:393 , LYS B:409 , LYS B:456 , ARG B:458 , HOH B:618 , HOH B:664 , HOH B:787BINDING SITE FOR RESIDUE SO4 B 602
6AC6SOFTWAREARG C:393 , LYS C:409 , LYS C:456 , ARG C:458 , MN C:550BINDING SITE FOR RESIDUE SO4 C 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D8H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D8H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D8H)

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL228W1YPL228W.1XVI:118382-1200311650CET1_YEAST1-5495493A:239-539 (gaps)
B:239-539 (gaps)
C:239-539 (gaps)		301
301
301

(-) 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:288
 aligned with CET1_YEAST | O13297 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:301
                                   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       508       518       528       538 
           CET1_YEAST   239 SKYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSY 539
               SCOP domains d1d8ha_ A: mRNA triphosphatase CET1                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1d8hA00 A:239-539 mRNA Triphosphatase Cet1; Chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh........ee...............ee..hhhhhhhhhhhhhhhhh....hhh.eeeeeeeeeee...............eee.....eeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..-----..eeeeeee.......eeeeeeeeeeeeee......eeeeeeeeeee....hhhhhhh......eeeeeeeeeee....eeeeeeeeee.--------.eeeeeeeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:239-539 (gaps) UniProt: 1-549 [INCOMPLETE]                                                                                                                                                                                                                                                   Transcript 1
                 1d8h A 239 HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVG-----PRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENH--------SETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSY 539
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378    |    -|      398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 
                                                                                                                                                                          383   389                                                                                      478      487                                                    


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with CET1_YEAST | O13297 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:301
                                   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       508       518       528       538 
           CET1_YEAST   239 SKYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSY 539
               SCOP domains d1d8hb_ B: mRNA triphosphatase CET1                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1d8hB00 B:239-539 mRNA Triphosphatase Cet1; Chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh........ee...............ee..hhhhhhhhhhhhhhhhhh...hhh.eeeeeeee..................eee...........hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..-----..eeeeeee.......eeeeeeeeeeeeee......eeeeeeeeeee....hhhhhhh......eeeeeeeeeeehhh.eeeeeeeeee.--------.eeeeeeeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:239-539 (gaps) UniProt: 1-549 [INCOMPLETE]                                                                                                                                                                                                                                                   Transcript 1
                 1d8h B 239 HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVG-----PRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENH--------SETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSY 539
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378    |    -|      398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 
                                                                                                                                                                          383   389                                                                                      478      487                                                    


Chain C from PDB  Type:PROTEIN  Length:288
 aligned with CET1_YEAST | O13297 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:301
                                   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       508       518       528       538 
           CET1_YEAST   239 SKYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSY 539
               SCOP domains d1d8hc_ C: mRNA triphosphatase CET1                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1d8hC00 C:239-539 mRNA Triphosphatase Cet1; Chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh........ee...............ee..hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee...............eee.....eeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee..-----..eeeeeee........eeeeeeeeeeeee......eeeeeeeeeee....hhhhhhh.....eeeeeeeeeeeehhh.eeeeeeeeee.--------.eeeeeeeeeehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:239-539 (gaps) UniProt: 1-549 [INCOMPLETE]                                                                                                                                                                                                                                                   Transcript 1
                 1d8h C 239 HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVG-----PRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENH--------SETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSY 539
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378    |    -|      398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 
                                                                                                                                                                          383   389                                                                                      478      487
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D8H)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CET1_YEAST | O13297)
molecular function
    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:0004651    polynucleotide 5'-phosphatase activity    Catalysis of the reaction: 5'-phosphopolynucleotide + H2O = polynucleotide + phosphate.
    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).
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0098507    polynucleotide 5' dephosphorylation    The process of removing one or more phosphate groups from the 5' end of a polynucleotide.
    GO:0098501    polynucleotide dephosphorylation    The process of removing one or more phosphate groups from a polynucleotide.
    GO:1900182    positive regulation of protein localization to nucleus    Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
cellular component
    GO:0031533    mRNA cap methyltransferase complex    A protein complex that consists of an RNA 5' triphosphatase and a guanyl transferase (Cet1p and Ceg1p in S. cerevisiae; Pct1 and Ceg1 in S. pombe) and is involved in mRNA capping.
    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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  1d8h
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  3.1.3.33
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 Related Entries

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

UniProtKB/Swiss-Prot
        CET1_YEAST | O13297: 1d8i 3kyh

(-) Related Entries Specified in the PDB File

1d8i