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(-) Description

Title :  STRUCTURAL BASIS FOR THE ACTIVITY OF A CYTOPLASMIC RNA TERMINAL U-TRANSFERASE
 
Authors :  L. A. Yates, S. Fleurdepine, O. S. Rissland, L. Decolibus, K. Harlos, C. J. Norbury, R. J. C. Gilbert
Date :  19 Mar 12  (Deposition) - 04 Jul 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta Polymerase-Like Nucleotidyl Transferase, Terminal Uridine Transferase, Utp, Rna, Cytoplasmic, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Yates, S. Fleurdepine, O. S. Rissland, L. De Colibus, K. Harlos, C. J. Norbury, R. J. Gilbert
Structural Basis For The Activity Of A Cytoplasmic Rna Terminal Uridylyl Transferase.
Nat. Struct. Mol. Biol. V. 19 782 2012
PubMed-ID: 22751018  |  Reference-DOI: 10.1038/NSMB.2329

(-) Compounds

Molecule 1 - POLY(A) RNA POLYMERASE PROTEIN CID1
    Chains: A, B, C, D
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: CID1, SPAC19D5.03
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE 972H-
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: CAFFEINE-INDUCED DEATH PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:279 , PHE A:283 , ARG A:351BINDING SITE FOR RESIDUE ACT A 501
2AC2SOFTWARETYR B:279 , PHE B:283 , PRO B:285 , ARG B:351BINDING SITE FOR RESIDUE ACT B 501
3AC3SOFTWARETYR C:279 , PHE C:283 , ARG C:351BINDING SITE FOR RESIDUE ACT C 501
4AC4SOFTWARETYR D:279 , PHE D:283 , ARG D:351BINDING SITE FOR RESIDUE ACT D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E7X)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Gly A:154 -Ala A:155
2Lys A:227 -Pro A:228
3Tyr A:366 -Pro A:367
4Lys B:227 -Pro B:228
5Tyr B:366 -Pro B:367
6Lys C:227 -Pro C:228
7Tyr C:366 -Pro C:367
8Lys D:227 -Pro D:228
9Tyr D:366 -Pro D:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E7X)

(-) Exons   (0, 0)

(no "Exon" information available for 4E7X)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhh.eeeeeeee..eeeeeeeee........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh........ee..............hhhhhhhhhhhhhhhhhhhh......hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e7x A   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPI  379
                                    50        60        70        80        90       100       115       125       135       145   ||  157       167       177       187       197      207A       217       227       237       247       257       267       277       287       297       307||     330       340       350       360       370         
                                                                                              109|                               149|                                                   207A                                                                                                  308|                                                         
                                                                                               115                                152                                                                                                                                                          322                                                         


Chain B from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhhh..eeeeee..eeeeee...eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh........ee........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4e7x B   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSSYPIPYDSLFEEAPIPP  381
                                    50        60        70        80        90       100       115       125       135       145 ||    165       175       185       195       205 |     215       225       235       245       255       265       275       285       295       305  ||   328       338       348       358    || 369       379  
                                                                                              109|                             147|                                             207A                                                                                                  308|                                      363|                
                                                                                               115                              158                                                                                                                                                    322                                       365                


Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhh...eeeeee..eeeeee.....eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh...........ee..............hhhhhhhhhhhhhhhhhhhh......hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e7x C   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSSFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPI  379
                                    50        60        70        80        90       100       115       125       135       145 ||    163       173       183       193       203   |   213       223       233       243       253       263       273       283       293       303       323       333       343       353       363       373      
                                                                                              109|                             147|                                               207A                                                                                                     311|                                                         
                                                                                               115                              156                                                                                                                                                         322                                                         


Chain D from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhh..eeeeeee..eeeeeeee.....eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh............ee..............hhhhhhhhhhhhhhhhhhhh......hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e7x D   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTSFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIP  380
                                    50        60        70        80        90       100       115       125       135       145   ||  161       171       181       191       201     | 211       221       231       241       251       261       271       281       291       301       311||     330       340       350       360       370       380
                                                                                              109|                               149|                                               207A                                                                                                      312|                                                          
                                                                                               115                                156                                                                                                                                                          322
   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 4E7X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E7X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E7X)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  4e7x
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  2.7.7.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        CID1_SCHPO | O13833: 4e80 4e8f 4ep7 4fh3 4fh5 4fhp 4fhv 4fhw 4fhx 4fhy 4nkt 4nku 4ud4 4ud5

(-) Related Entries Specified in the PDB File

4e80 UTP-BOUND STRUCTURE.
4e8f ACETATE BOUND FORM.