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(-) Description

Title :  CRYSTAL STRUCTURE OF THG1 LIKE PROTEIN (TLP) WITH TRNA(PHE) AND GDPNP
 
Authors :  S. Kimura, T. Suzuki, J. Yu, K. Kato, M. Yao
Date :  31 Jul 15  (Deposition) - 03 Aug 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,P
Biol. Unit 1:  A,B,P  (2x)
Keywords :  Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kimura, T. Suzuki, M. Chen, K. Kato, J. Yu, A. Nakamura, I. Tanaka, M. Yao
Template-Dependent Nucleotide Addition In The Reverse (3'-5') Direction By Thg1-Like Protein
Sci Adv V. 2 01397 2016
PubMed-ID: 27051866  |  Reference-DOI: 10.1126/SCIADV.1501397

(-) Compounds

Molecule 1 - TRNA(HIS)-5'-GUANYLYLTRANSFERASE (THG1) LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET26B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOSARCINA ACETIVORANS
    Organism Taxid: 2214
 
Molecule 2 - RNA (75-MER)
    Chains: P
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABP
Biological Unit 1 (2x): ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3MG5Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , ASP A:69 , MG A:302 , GNP A:304 , GTP P:2binding site for residue MG A 301
2AC2SOFTWAREASP A:21 , GLY A:22 , ASP A:69 , MG A:301 , GTP P:2binding site for residue MG A 302
3AC3SOFTWAREGNP A:304 , HOH A:401 , HOH A:406 , LYS B:86 , HOH P:102binding site for residue MG A 303
4AC4SOFTWAREARG A:19 , ARG A:114 , GLU A:133 , MG A:301 , MG A:303 , HOH A:401 , HOH A:404 , ARG B:83 , LYS B:86 , GTP P:2 , C P:72binding site for residue GNP A 304
5AC5SOFTWAREASP B:21 , GLY B:22 , ARG B:23 , ASN B:24 , PHE B:25 , LYS B:26 , GLU B:35 , PRO B:37 , ASP B:39 , PHE B:42 , SER B:68 , ASP B:69 , MG B:302 , MG B:303 , HOH B:403binding site for residue GNP B 301
6AC6SOFTWAREASP B:21 , GLY B:22 , ASP B:69 , GNP B:301binding site for residue MG B 302
7AC7SOFTWAREASP B:21 , GNP B:301 , HOH B:403binding site for residue MG B 303
8AC8SOFTWAREASP A:21 , GLY A:22 , ASN A:24 , PHE A:25 , LYS A:26 , ASP A:69 , TYR A:144 , ALA A:158 , MG A:301 , MG A:302 , GNP A:304 , HOH A:405 , G P:4 , C P:70 , C P:71 , HOH P:101 , HOH P:102binding site for Di-nucleotide GTP P 2 and G P 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AXN)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:14 -Pro A:15
2Lys A:36 -Pro A:37
3Ser A:68 -Asp A:69
4Glu A:230 -Lys A:231
5Pro B:14 -Pro B:15
6Lys B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AXN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AXN)

(-) Exons   (0, 0)

(no "Exon" information available for 5AXN)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeee.hhhhhh.........hhhhhhhhhhhhhhhhhhh......eeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhh.eeee....eee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5axn A   1 MKTREIYAEMRCIPPVVLRADGRNFKNTLSGLGFEKPYDKTFARAMADTAELFIKKSGLSPLFAYTFSDEISFLFTDLPFDGRVEKIDSVVASFLGSALTIKLRLEEPIAFDSRLVALQKEEIPEYFHRRQLEAWRNFVASWGYYALRNMGRNEAAKYLKRKKESEIHEMLFERGINLATLPSWQRRGVIISKRKITQNWEIPKFKSEKGIPFLEKLIN 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       152       162       172       182       192  ||   222       232         
                                                                                                                                                                              149|                                        195|                         
                                                                                                                                                                               152                                         216                         


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......eeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhheeeeeeeeeeeeee....eeeeeeeeeeeee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5axn B   3 TREIYAEMRCIPPVVLRADGRNFKNTLSGLGFEKPYDKTFARAMADTAELFIKKSGLSPLFAYTFSDEISFLFTDLPFDGRVEKIDSVVASFLGSALTIKLRLEEPIAFDSRLVALQKEEIPEYFHRRQLEAWRNFVASWGYYALRNEGMGRNEAAKYLKRKKESEIHEMLFERGINLATLPSWQRRGVIISKEAREIQGFNPVSGKEEKSLRRKITQNWEIPKFKSEKGIPFLEKLIN 241
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         


Chain P from PDB  Type:RNA  Length:66
                                                                                                  
                 5axn P   2 xGGAUUUAGCUCAGUUGGGAGAGCGCCAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUCCCCAC  74
                            |       11        21        38        48        58        68      
                            2-GTP                      30|                                    
                                                        38
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5AXN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AXN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AXN)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5AXN)

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 Related Entries

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        A0A1C7D1G9_9 | A0A1C7D1G9: 5axk 5axl 5axm

(-) Related Entries Specified in the PDB File

5axk 5axl 5axm