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(-) Description

Title :  STRUCTURE OF CID1 IN COMPLEX WITH ITS SHORT PRODUCT APU
 
Authors :  P. Munoz-Tello, C. Gabus, S. Thore
Date :  13 Nov 13  (Deposition) - 18 Dec 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,D,H
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,H  (1x)
Keywords :  Poly(U) Polymerase, Nucleotidyl Tranfer Domain, Pap-Associated Domain, Utp Binding, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Munoz-Tello, C. Gabus, S. Thore
A Critical Switch In The Enzymatic Properties Of The Cid1 Protein Deciphered From Its Product-Bound Crystal Structure
Nucleic Acids Res. V. 42 3372 2014
PubMed-ID: 24322298  |  Reference-DOI: 10.1093/NAR/GKT1278

(-) 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 Plasmid: PET42-BASED
    Expression System Strain: BL21 STAR
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 40-377
    Gene: CID1, SPAC19D5.03
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: CAFFEINE-INDUCED DEATH PROTEIN 1
 
Molecule 2 - 5'-R(*AP*U)-3'
    Chains: D, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDH
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B H

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1BR3Ligand/IonBROMIDE ION
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:517 , HOH A:619 , HOH A:680BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWARETHR A:45 , HOH A:573BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARELEU B:74 , HOH B:644BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWARELYS B:193 , HOH B:593 , U H:59BINDING SITE FOR RESIDUE BR B 402
5AC5SOFTWARELYS A:193 , HOH A:609 , U D:59BINDING SITE FOR RESIDUE BR D 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:227 -Pro A:228
2Lys B:227 -Pro B:228
3Tyr B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NKU)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee...hhhhhhhhhhhh.eeeee........eeeeee..........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh.......................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nku A  38 DMSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA 377
                                    47        57        67        77        87        97       107 ||    123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    || 327       337       347       357       367       377
                                                                                                 109|                                                                                                                                                                                             308|                                                      
                                                                                                  116                                                                                                                                                                                              323                                                      


Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee...hhhhhhhhhhhh..eeeee...eeeeee..eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh..........ee........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nku B  39 MSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDTIALQFYEELIAEGFEGKFLQIPIIKLTSFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA 377
                                    48        58        68        78        88        98       108||     124       134 ||    147|      166       176       186       196       206       216       226       236       246       256       266       276       286       296       306   ||  327       337       347       357       367       377
                                                                                                109|                 136|    147|                                                                                                                                                      310|                                                       
                                                                                                 116                  140     157                                                                                                                                                       322                                                       


Chain D from PDB  Type:RNA  Length:2
                                  
                 4nku D  58 AU  59


Chain H from PDB  Type:RNA  Length:2
                                  
                 4nku H  58 AU  59
   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 4NKU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  4nku
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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 4e8f 4ep7 4fh3 4fh5 4fhp 4fhv 4fhw 4fhx 4fhy 4nkt 4ud4 4ud5

(-) Related Entries Specified in the PDB File

4nkt