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(-) Description

Title :  CRYSTAL STRUCTURE OF O-PHOSPHOSERYL-TRNA KINASE COMPLEXED WITH ANTICODON-STEM/LOOP TRUNCATED TRNA(SEC)
 
Authors :  Y. Araiso, R. Ishitani, O. Nureki
Date :  11 Aug 10  (Deposition) - 29 Dec 10  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Kinase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Sherrer, Y. Araiso, C. Aldag, R. Ishitani, J. M. L. Ho, D. Soll, O. Nureki
C-Terminal Domain Of Archaeal O-Phosphoseryl-Trna Kinase Displays Large-Scale Motion To Bind The 7-Bp D-Stem Of Archaeal Trna(Sec)
Nucleic Acids Res. V. 39 1034 2011
PubMed-ID: 20870747  |  Reference-DOI: 10.1093/NAR/GKQ845

(-) Compounds

Molecule 1 - L-SERYL-TRNA(SEC) KINASE
    Chains: A
    EC Number: 2.7.1.164
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PSTK, MJ1538
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: O-PHOSPHOSERYL-TRNA(SEC) KINASE, PSTK
 
Molecule 2 - ASL-TRUNCATED TRNA
    Chains: B
    Engineered: YES
    Other Details: SYNTHESIZED RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:13 , GLY A:14 , VAL A:15 , GLY A:16 , LYS A:17 , SER A:18 , THR A:19 , ARG A:116 , THR A:154 , MG A:401BINDING SITE FOR RESIDUE ATP A 301
2AC2SOFTWARESER A:18 , ATP A:301BINDING SITE FOR RESIDUE MG A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AM1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AM1)

(-) Exons   (0, 0)

(no "Exon" information available for 3AM1)

(-) 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:236
 aligned with PSTK_METJA | Q58933 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:250
                              1                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
           PSTK_METJA     - --MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKEFKDLLNSY 248
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeee.hhhhhh.......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhh....hhhhhhhhhhhh.............eeee.....hhhhhhhhhhhhhh.....-----------hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh---.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3am1 A   3 DIMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKF-----------NISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKK---VDADRVLKEFKDLLNSY 252
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172    |    -      |192       202       212       222       232   |   242       252
                                                                                                                                                                                                        177         189                                        232 236                


Chain B from PDB  Type:RNA  Length:81
                                                                                                                 
                 3am1 B   1 GGCGCGGGGUACCGGGCUUGGUAGCCCGGGGCUUCGGCCGAGGGCGAGAGCCCUCGGGGUUCGAUUCCCCCCCUGCGCCGC  81
                                    10        20        30        40        50        60        70        80
   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 3AM1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AM1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PSTK_METJA | Q58933)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0097056    selenocysteinyl-tRNA(Sec) biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine.

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  2.7.1.164
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 Related Entries

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

UniProtKB/Swiss-Prot
        PSTK_METJA | Q58933: 3a4l 3a4m 3a4n 3adb 3adc 3add

(-) Related Entries Specified in the PDB File

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