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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A.FULGIDUS CCA-ADDING ENZYME IN COMPLEX WITH A G70A ARGINYL-TRNA MINIHELIX ENDING IN CCACCA
 
Authors :  C. -D. Kuhn, L. Joshua-Tor
Date :  03 Dec 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I
Keywords :  Protein-Rna Complex, Trna, Non-Coding Rna, Cca-Adding Enzyme, Nucleotidyltransferase, Ncrna, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Kuhn, J. E. Wilusz, Y. Zheng, P. A. Beal, L. Joshua-Tor
On-Enzyme Refolding Permits Small Rna And Trna Surveillance By The Cca-Adding Enzyme.
Cell V. 160 644 2015
PubMed-ID: 25640237  |  Reference-DOI: 10.1016/J.CELL.2015.01.005

(-) Compounds

Molecule 1 - CCA-ADDING ENZYME
    Chains: A, C, E, F
    EC Number: 2.7.7.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22
    Expression System Strain: BL21(DE3)RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CCA, AF_2156
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS (STRAIN ATCC 49558 / VC- 16 / DSM 4304 / JCM 9628 / NBRC 100126)
    Organism Taxid: 224325
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
    Synonym: CCA TRNA NUCLEOTIDYLTRANSFERASE,TRNA CCA-PYROPHOSPHORYLASE, TRNA ADENYLYL-/CYTIDYLYL- TRANSFERASE,TRNA NUCLEOTIDYLTRANSFERASE, TRNA-NT
 
Molecule 2 - G70A TRNA MINIHELIX ENDING IN CCACCA
    Chains: B, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - G70A TRNA MINIHELIX ENDING IN CCACCA
    Chains: G
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 4 - RNA (5'-D(P*CP*G)-3')
    Chains: H
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 5 - RNA (5'-D(P*GP*G)-3')
    Chains: I
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit : ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
15BU6Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2GOL3Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:282 , SER A:323 , PHE A:326 , TYR A:328 , PRO A:424 , LYS F:357binding site for residue GOL A 501
2AC2SOFTWAREGLU A:311 , ARG A:380 , LYS A:381binding site for residue GOL A 502
3AC3SOFTWAREVAL A:271 , THR A:276 , VAL A:278 , GLU A:386 , HOH A:623binding site for residue GOL A 503
4AC4SOFTWAREARG A:361 , GLU A:378 , LYS A:381 , ARG E:284binding site for residue PEG E 501
5AC5SOFTWARETYR E:165 , ARG E:224 , ALA E:228 , ASN E:229 , ALA F:163 , TYR F:165 , ARG F:224 , ALA F:228 , ASN F:229 , ASP F:291 , G G:2 , C G:3 , C G:4 , C G:6 , G G:7 , G G:8 , C G:9 , C G:24 , C G:25 , G G:26 , G G:28 , C G:31 , HOH G:102 , HOH G:104 , HOH G:105 , HOH G:107binding site for Di-nucleotide A G 29 and 5BU G 30
6AC6SOFTWAREALA E:163 , TYR E:165 , ARG E:224 , ALA E:228 , ASN E:229 , ASP E:291 , GLU F:96 , ALA F:163 , TYR F:165 , ARG F:224 , ASP F:291 , G G:1 , G G:2 , G G:7 , G G:8 , C G:9 , G G:23 , G G:29 , A G:29 , HOH G:102 , HOH G:104 , HOH G:106 , HOH G:107binding site for Di-nucleotide 5BU G 30 and C G 31

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X4T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X4T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X4T)

(-) Exons   (0, 0)

(no "Exon" information available for 4X4T)

(-) 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:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhh.........eeeeeee.....hhhhhhhhhhhhhh.....eee.....eeeeee..eeeeeeeee.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4t A   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       


Chain B from PDB  Type:RNA  Length:34
                                                                  
                 4x4t B   1 GGCCGCGGCAGGxUCGAAUCCxGCCGCGAxCGCC  34
                                    10  |     20 |      30    
                                       13-5BU   22-5BU  30-5BU


Chain C from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh.........eeeeeee......hhhhhhhhhhhhh...eeeeee...eeeeeee..eeeeeeeee.............hhhhhhhhhh.....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4t C   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       


Chain D from PDB  Type:RNA  Length:30
                                                              
                 4x4t D   1 GGCCGCGGCAGGxUCGAUCCxGCCGCGGCC  34
                                    10  |   ||21|     ||34
                                       13-5BU|  |    28|  
                                            19  |     32  
                                               22-5BU     


Chain E from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeehhhhh.........eeeeeee....hhhhhhhhhhhhhhhhheeeeeee...eeeeeee..eeeeeeeee...hhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4t E   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       


Chain F from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh........eeeeeeee....hhhhhhhhhhhhhhhhh.eeeeee...eeeeeee..eeeeeeeee...hhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4t F   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       


Chain G from PDB  Type:RNA  Length:20
                                                    
                 4x4t G   1 GGCCGCGGCGCCGCGAGxCC  31
                                    23       |31
                                    9|      30-5BU
                                    23          


Chain H from PDB  Type:RNA  Length:2
                                  
                 4x4t H   1 CG   2


Chain I from PDB  Type:RNA  Length:2
                                  
                 4x4t I   1 GG   2
   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 4X4T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X4T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X4T)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4x4t
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 Related Entries

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

UniProtKB/Swiss-Prot
        CCA_ARCFU | O28126: 1r89 1r8a 1r8b 1r8c 1sz1 1tfw 1tfy 1uet 1ueu 1uev 2dr5 2dr7 2dr8 2dr9 2dra 2drb 2dvi 2zh1 2zh2 2zh3 2zh4 2zh5 2zh6 2zh7 2zh8 2zh9 2zha 2zhb 3ouy 3ov7 3ova 3ovb 3ovs 4x4n 4x4o 4x4p 4x4q 4x4r 4x4s 4x4u 4x4v

(-) Related Entries Specified in the PDB File

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