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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA NUCLEOTIDYLTRANSFERASE COMPLEXED WITH A PRIMER TRNA AND AN INCOMING ATP ANALOG
 
Authors :  K. Tomita, S. Fukai, R. Ishitani, T. Ueda, N. Takeuchi, D. G. Vassylyev, O. Nureki, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Apr 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Transferase, Rna, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tomita, S. Fukai, R. Ishitani, T. Ueda, N. Takeuchi, D. G. Vassylyev, O. Nureki
Structural Basis For Template-Independent Rna Polymerization.
Nature V. 430 700 2004
PubMed-ID: 15295603  |  Reference-DOI: 10.1038/NATURE02712
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (75-MER)
    Chains: C, D
    Engineered: YES
    Other Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE IN THERMOTOGA MARITIMA
    Synthetic: YES
 
Molecule 2 - POLY A POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-390
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: A-ADDING ENZYME

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , ARG A:21 , ASP A:22 , ARG A:104 , ASP A:105 , ASP A:149 , ARG A:152 , ARG A:155 , ARG A:158 , ARG A:162 , ARG A:191 , HOH A:501 , HOH A:505 , HOH A:520BINDING SITE FOR RESIDUE APC A 500
2AC2SOFTWAREGLY B:18 , ARG B:21 , ARG B:103 , ASP B:105 , ASN B:109 , ASP B:149 , ARG B:152 , ARG B:155 , ARG B:158 , PHE B:159 , ARG B:162 , C D:75 , HOH D:82BINDING SITE FOR RESIDUE APC B 1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VFG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VFG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VFG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VFG)

(-) Exons   (0, 0)

(no "Exon" information available for 1VFG)

(-) 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:342
 aligned with O66728_AQUAE | O66728 from UniProtKB/TrEMBL  Length:824

    Alignment length:351
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791 
         O66728_AQUAE   442 EVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARRETYPRPGAYPKVEPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKLP 792
               SCOP domains d1vfga2 A:1-136 Poly A polymerase PcnB                                                                                                  d1vfga1 A:137-351 Poly A polymerase PcnB                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...eeeehhhhhhhhh.....eeeeee..hhhhhhhhhhhhhh...eee....eeeeee..eeeeeee.....---------....hhhhhhhh..hhhhh.eee.hhhhh..ee...hhhhhhhh.ee.....hhhhhh.hhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfg A   1 MVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARRET---------VEPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKLP 351
                                    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 
                                                                                                            82        92                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:358
 aligned with O66728_AQUAE | O66728 from UniProtKB/TrEMBL  Length:824

    Alignment length:373
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811   
         O66728_AQUAE   442 EVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARRETYPRPGAYPKVEPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKLPKEKIEELKKQGLKGKELGERIE 814
               SCOP domains d1vfgb2 B:1-136 Poly A polymerase PcnB                                                                                                  d1vfgb1 B:137-351 Poly A polymerase PcnB                                                                                                                                                                                     ---------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------PolyA_pol-1vfgB01 B:13-139                                                                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      ---------------- Pfam domains (1)
           Pfam domains (2) ------------PolyA_pol-1vfgB02 B:13-139                                                                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      ---------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhh...eeeehhhhhhhhh.....eeeeee..hhhhhhhhhhhhhh...eee....eeeeee..eeeeeee.....---------....hhhhhhhh..hhhhh.eee.hhhhh..ee...hhhhhhhh.ee.....hhhhhh.hhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..------.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfg B   1 MVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPEFGTAHLKIGKLKLEFATARRET---------VEPASLKEDLIRRDFTINAMAISVNLEDYGTLIDYFGGLRDLKDKVIRVLHPVSFIEDPVRILRALRFAGRLNFKLSRSTEKLLKQAVNLGLLKEAPRGRLINEIKLALREDRFLEILELYRKYRVLEEIIEGFQWNEKVLQKLYALRKVVDWHALEFSEERIDYGWLYLLILISNLDYERGKHFLEEMSAPSWVRETYKFMKFKLGSLKEELKKAKENYEVYRLLKPLHTSVLLLLMLEEELKEKIKLYLEKLRKVKLP------LKREIMNKIKLAAALE 390
                                    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|      377       387   
                                                                                                            82        92                                                                                                                                                                                                                                                                351    375               


Chain C from PDB  Type:RNA  Length:31
                                                               
                 1vfg C   1 GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCC  72
                                  ||51        61        71 
                                  7|                       
                                  49                       


Chain D from PDB  Type:RNA  Length:34
                                                                  
                 1vfg D   1 GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCACC  75
                                  ||51        61        71    
                                  7|                          
                                  49
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VFG)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NTP_transf (45)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O66728_AQUAE | O66728)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.

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  1vfg
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  2.7.7.19
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 Related Entries

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

UniProtKB/TrEMBL
        O66728_AQUAE | O66728: 4wby 4wbz 4wc0 4wc1 4wc2 4wc3 4wc4 4wc5 4wc6 4wc7 4x0a 4x0b

(-) Related Entries Specified in the PDB File

1miw
1ou5
1r89 RELATED ID: AR_001000505.1 RELATED DB: TARGETDB
1uet