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(-) Description

Title :  TRNA-PROCESSING ENZYME WITH ATP
 
Authors :  S. Yamashita, K. Tomita
Date :  04 Sep 14  (Deposition) - 15 Apr 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna Nucleotidyltransferase, Cca-Adding Enzyme, A-Adding Enzyme, Transferase (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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    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

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , GLY A:18 , ARG A:21 , ARG A:104 , ASP A:105 , ASN A:109 , ASP A:149 , ARG A:152 , ARG A:155 , ARG A:162 , ARG A:191 , MG A:402binding site for residue ATP A 401
2AC2SOFTWAREATP A:401binding site for residue MG A 402
3AC3SOFTWAREGLY B:17 , GLY B:18 , ARG B:21 , ARG B:104 , ASP B:105 , ASN B:109 , ASP B:149 , ARG B:152 , ARG B:155 , ARG B:158 , PHE B:159 , ARG B:162 , ARG B:191 , MG B:402binding site for residue ATP B 401
4AC4SOFTWAREATP B:401binding site for residue MG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WC0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WC0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WC0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WC0)

(-) Exons   (0, 0)

(no "Exon" information available for 4WC0)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..eeeeehhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhh..eeee....eeeeee..eeeeeee......hhhhhhhh..hhhhh.eee........ee...hhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wc0 A   1 MVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARREPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKLPKEKIEELKKELGERIEELKREIMNK 382
                                    10        20        30        40        50        60        70        80||     102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       368       378    
                                                                                                           81|                                                                                                                                                                                                                                                                       360|               
                                                                                                            94                                                                                                                                                                                                                                                                        367               


Chain B from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.eeeeehhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhh...eee....eeeeee..eeeeeee......hhhhhhhh..hhhhh.eee........ee...hhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wc0 B   1 MVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARREPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKERIEELKREIMNK 382
                                    10        20        30        40        50        60        70        80||     102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      |372       382
                                                                                                           81|                                                                                                                                                                                                                                                            349|            
                                                                                                            94                                                                                                                                                                                                                                                             370
   Legend:   → Mismatch (orange background)
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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 4WC0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WC0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WC0)

(-) Gene Ontology  (7, 7)

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  4wc0
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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 4wc1 4wc2 4wc3 4wc4 4wc5 4wc6 4wc7 4x0a 4x0b

(-) Related Entries Specified in the PDB File

1vfg 1VFG CONTAINS THE SAME PROTEIN COMPLEXED WITH TRNA.
4wby
4wbz
4wc1
4wc2
4wc3
4wc4
4wc5
4wc6
4wc7