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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 :  20 Mar 12  (Deposition) - 04 Jul 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:168 , ASN A:171BINDING SITE FOR RESIDUE ACT A 500
2AC2SOFTWAREILE B:57 , HOH B:630BINDING SITE FOR RESIDUE GOL B 500
3AC3SOFTWAREASP A:258 , PRO A:261 , SER B:90 , LEU B:91 , SER B:176BINDING SITE FOR RESIDUE ACT B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E8F)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Lys A:227 -Pro A:228
2Tyr A:366 -Pro A:367
3Asn B:39 -Ser B:40
4Leu B:91 -Glu B:92
5Lys B:227 -Pro B:228
6Tyr B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E8F)

(-) Exons   (0, 0)

(no "Exon" information available for 4E8F)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee.....hhhhhhhhhhhhh.eeeeeeee..eeeeeeeee..........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh........ee..............hhhhhhhhhhhhhhhhhhhh......hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e8f A  38 PNSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSSDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIP 380
                                    47        57        67        77        87        97       107  ||   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       323       333       343       353       363       373       
                                                                                                  110|                                                                                                                                                                                               308|                                                          
                                                                                                   114                                                                                                                                                                                                322                                                          


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeee...............eeeee....hhhhhhhhhhhhh.eeeeeeee..eeeeeeeee..........eeeeeeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh........ee..............hhhhhhhhhhhhhhhhhhhhh.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e8f B  38 PNSHKEFTKFCYEVYNEIKIKRAALDTLRLCLKRISPDAELVAFSLESGLALKNSDMDLCVLMDSRDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIP 380
                                    47        57|       74        84   ||   95       105     ||118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308|      331       341       351       361       371         
                                              57|                     88|                  111|                                                                                                                                                                                              308|                                                          
                                               65                      90                   115                                                                                                                                                                                               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 4E8F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E8F)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  4e8f
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  CID1_SCHPO | O13833
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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: 4e7x 4e80 4ep7 4fh3 4fh5 4fhp 4fhv 4fhw 4fhx 4fhy 4nkt 4nku 4ud4 4ud5

(-) Related Entries Specified in the PDB File

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