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(-) Description

Title :  THE MOLECULAR ARCHITECTURE OF THE TRAMP COMPLEX REVEALS THE ORGANIZATION AND INTERPLAY OF ITS TWO CATALYTIC ACTIVITIES
 
Authors :  S. Falk, J. R. Weir, J. Hentschel, P. Reichelt, F. Bonneau, E. Conti
Date :  23 Jul 14  (Deposition) - 24 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helicase, Atpase, Poly(A)Polymerase, Rna Degradation, Exosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Falk, J. R. Weir, J. Hentschel, P. Reichelt, F. Bonneau, E. Conti
The Molecular Architecture Of The Tramp Complex Reveals The Organization And Interplay Of Its Two Catalytic Activities.
Mol. Cell V. 55 856 2014
PubMed-ID: 25175027  |  Reference-DOI: 10.1016/J.MOLCEL.2014.07.020

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DOB1
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: PLYSS
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 81-1073
    Gene: MTR4, DOB1, YJL050W, J1158
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: MRNA TRANSPORT REGULATOR MTR4
 
Molecule 2 - PROTEIN AIR2,POLY(A) RNA POLYMERASE PROTEIN 2
    Chains: B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: PLYSS
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1-62,UNP RESIDUES 111-160,UNP RESIDUES 1-62, UNP RESIDUES 111-160
    Gene: AIR2, YDL175C, PAP2, TRF4, YOL115W, HRC584, O0716
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Other Details: FUSION OF AIR2 RESIDUES 1-62 TO TRF4 RESIDUES 111-160
    Strain: ATCC 204508 / S288C
    Synonym: ARGININE METHYLTRANSFERASE-INTERACTING RING FINGER PROTEIN 2,DNA POLYMERASE KAPPA,DNA POLYMERASE SIGMA,TOPOISOMERASE 1-RELATED PROTEIN TRF4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5SO47Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:883 , ARG A:884 , ARG A:887binding site for residue SO4 A 1101
02AC2SOFTWARETHR A:173 , GLY A:176 , LYS A:177 , THR A:178 , HOH A:1277binding site for residue SO4 A 1102
03AC3SOFTWARELYS A:864 , ARG A:883 , LYS A:886 , ARG A:890 , ASP A:899binding site for residue SO4 A 1103
04AC4SOFTWAREARG A:774 , ARG A:954 , THR B:15binding site for residue SO4 A 1104
05AC5SOFTWARELYS A:768binding site for residue SO4 A 1105
06AC6SOFTWAREHIS A:476 , SER A:477 , THR A:502 , THR A:504binding site for residue SO4 A 1106
07AC7SOFTWAREARG A:887 , ARG A:890binding site for residue SO4 A 1107
08AC8SOFTWAREHIS A:647binding site for residue EDO A 1108
09AC9SOFTWAREALA A:214 , GLU A:215 , GLY A:217binding site for residue EDO A 1109
10AD1SOFTWARELYS A:437 , HOH A:1402binding site for residue CL A 1110
11AD2SOFTWARELYS A:202 , ARG A:1026binding site for residue CL A 1111
12AD3SOFTWAREGLU A:142 , LEU A:150 , ASP A:155 , GLY A:785 , THR A:789 , HOH A:1222 , HOH A:1399binding site for residue PG4 A 1112
13AD4SOFTWAREGLY A:224 , THR A:227 , LYS A:1036 , HIS A:1062 , HOH A:1285binding site for residue PG4 A 1113
14AD5SOFTWAREPHE A:491 , GLY A:494 , PRO A:512 , ARG A:546binding site for residue PEG A 1114

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U4C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:407 -Pro A:408

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U4C)

(-) Exons   (0, 0)

(no "Exon" information available for 4U4C)

(-) 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:924
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee........hhhhh.............hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeee....ee.....eeeeehhhhhhhhhh..hhhhheeeeee.hhhhhhh..hhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhh..eeeeee......eeeeeee....eeeeee......hhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh....eeee.hhhhhh......eeee...eee....eee.hhhhhhhhhh..........eeeeeee....hhhhhhhhhh............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhheeeeeeeeeeeee.....hhhh.eeeeeeeeeee...hhhhh...................eeeeeeeee...eeeeeeee..........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4u4c A  117 HQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL 1073
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      |393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703|      719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069    
                                                                                                                                                                                                                                                                                363|                                                                                                                                                                                                                                                                                                                     703|                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                 391                                                                                                                                                                                                                                                                                                                      710                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:56
                                                                                         
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee..hhhhh..hhhhhhhhhh..............eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                4u4c B    5 TAPFVVDTAPTTPPDKLVAPSIEEVNSNPNELRALRGQGRYFGVSDDDNDDFISLS  127
                                    14        24        34        44       121      
                                                                          52|       
                                                                          120
   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 4U4C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U4C)

(-) Gene Ontology  (51, 80)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AIR2_YEAST | Q12476: 2lli 3nyb
        MTR4_YEAST | P47047: 2xgj 4qu4 4wfd
        PAP2_YEAST | P53632: 2mow 3nyb

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