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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA NUCLEOTIDYLTRANSFERASE COMPLEXED WITH A PRIMER TRNA AND AN INCOMING ATP ANALOG
 
Authors :  S. Yamashita, K. Tomita
Date :  04 Sep 14  (Deposition) - 15 Apr 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Nucleotidyltransferase, Cca-Adding Enzyme, A-Adding Enzyme, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamashita, A. Martinez, K. Tomita
Measurement Of Acceptor-T Psi C Helix Length Of Trna For Terminal A76-Addition By A-Adding Enzyme.
Structure V. 23 830 2015
PubMed-ID: 25914059  |  Reference-DOI: 10.1016/J.STR.2015.03.013

(-) Compounds

Molecule 1 - POLY A POLYMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 443-824
    Gene: PCNB1, AQ_411
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: A-ADDING ENZYME
 
Molecule 2 - RNA 75-MER
    Chains: B
    Engineered: YES
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Other Details: TRNAPHE FROM THERMOTOGA MARITIMA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , ARG A:21 , ARG A:104 , ASP A:105 , ASN A:109 , ASP A:149 , ARG A:152 , ARG A:155 , ARG A:158 , PHE A:159 , ARG A:162 , MG A:402 , C B:75binding site for residue APC A 401
2AC2SOFTWAREAPC A:401binding site for residue MG A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WC2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WC2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WC2)

(-) Exons   (0, 0)

(no "Exon" information available for 4WC2)

(-) 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    
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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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeeehhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhh..eeee....eeeeee..eeeeeee........hhhhhhh...hhhhh.eee........ee...hhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wc2 A   1 MVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARRETEPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKLPKEKIEELKKGKELGERIEELKREIMN 381
                                    10        20        30        40        50        60        70        80 ||    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|      374       
                                                                                                            82|                                                                                                                                                                                                                                                                        360|                
                                                                                                             93                                                                                                                                                                                                                                                                         365                


Chain B from PDB  Type:RNA  Length:75
                                                                                                           
                 4wc2 B   1 GGCCAGGUAGCUCAGUUGGUAGAGCACUGGACUGAAAAUCCAGGUGUCGGCGGUUCGAUUCCGCCCCUGGCCACC  75
                                    10        20        30        40        50        60        70
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  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 4WC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WC2)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  O66728_AQUAE | O66728
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 Related Entries

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

UniProtKB/TrEMBL
        O66728_AQUAE | O66728: 1vfg 4wby 4wbz 4wc0 4wc1 4wc3 4wc4 4wc5 4wc6 4wc7 4x0a 4x0b

(-) Related Entries Specified in the PDB File

1vfg AUTHORS STATE THE MTZ FILE WAS DOWNLOADED FROM PDB DATABASE (AND SPACE GROUP WAS CONVERGED FROM P2 TO P21212). USING THE HIGH RESOLUTION APO STRUCTURE AND RECENT EXCELLENT PROGRAMS, AUTHORS COULD IMPROVED THE MODEL SO MUCH.
4wby
4wbz
4wc0
4wc1
4wc3
4wc4
4wc5
4wc6
4wc7