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(-) Description

Title :  STRUCTURE OF CID1 IN COMPLEX WITH THE UTP ANALOG UMPNPP
 
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 :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Poly(U) Polymerase, Nucleotidyl Tranfer Domain, Pap-Associated Domain, Utp Binding, Transferase (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

 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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
12KH2Ligand/Ion5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE
2BR3Ligand/IonBROMIDE ION
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12KH1Ligand/Ion5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE
2BR-1Ligand/IonBROMIDE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12KH1Ligand/Ion5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE
2BR-1Ligand/IonBROMIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:88 , GLY A:89 , SER A:90 , ASP A:103 , ALA A:168 , ASN A:171 , THR A:172 , LYS A:193 , LYS A:197 , ASN A:202 , SER A:210 , SER A:211 , TYR A:212 , HIS A:336 , BR A:403 , MG A:404 , HOH A:512 , HOH A:532 , HOH A:537 , HOH A:562 , HOH A:583 , HOH A:628 , HOH A:673 , HOH A:688 , HOH A:701 , HOH A:772 , HOH A:792 , HOH A:793BINDING SITE FOR RESIDUE 2KH A 401
2AC2SOFTWAREARG A:277 , HOH A:784BINDING SITE FOR RESIDUE BR A 402
3AC3SOFTWARE2KH A:401BINDING SITE FOR RESIDUE BR A 403
4AC4SOFTWAREASN A:165 , 2KH A:401BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWAREPHE B:88 , GLY B:89 , SER B:90 , ASP B:101 , ALA B:168 , ASN B:171 , THR B:172 , LYS B:193 , LYS B:197 , ASN B:202 , SER B:210 , SER B:211 , TYR B:212 , HIS B:336 , BR B:402 , MG B:404 , HOH B:507 , HOH B:546 , HOH B:573 , HOH B:648 , HOH B:658 , HOH B:693BINDING SITE FOR RESIDUE 2KH B 401
6AC6SOFTWARE2KH B:401BINDING SITE FOR RESIDUE BR B 402
7AC7SOFTWAREASN B:362BINDING SITE FOR RESIDUE MG B 403
8AC8SOFTWAREASN B:165 , 2KH B:401BINDING SITE FOR RESIDUE MG B 404
9AC9SOFTWARETHR B:45BINDING SITE FOR RESIDUE MG B 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:227 -Pro A:228
2Tyr A:366 -Pro A:367
3Lys B:227 -Pro B:228
4Tyr B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NKT)

(-) 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 ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee..hhhhhhhhhhhh.eeeee........eeeeee..........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh.......................hhhhhhhhhhhhhhhhhhhh......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nkt A  38 DMSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA 377
                                    47        57        67        77        87        97       107||     124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   ||  328       338       348       358       368         
                                                                                                108|                                                                                                                                                                                             308|                                                      
                                                                                                 116                                                                                                                                                                                              323                                                      


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee..hhhhhhhhhhh...eeeee...eeeeee...eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nkt B  38 DMSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMTIALQFYEELIAEGFEGKFLQIPIIKLTSSFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA 377
                                    47        57        67        77        87        97       107||     124       134 ||    147|      165       175       185       195       205       215       225       235       245       255       265       275       285       295       305  ||   329       339       349       359       369        
                                                                                                108|                 136|    147|                                                                                                                                                     308|                                                      
                                                                                                 116                  140     156                                                                                                                                                      323
   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 4NKT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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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 4nku 4ud4 4ud5

(-) Related Entries Specified in the PDB File

4nku