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(-) Description

Title :  CRYSTAL STRUCTURE OF O-PHOSPHOSERYL-TRNA KINASE COMPLEXED WITH SELENOCYSTEINE TRNA AND AMPPNP (CRYSTAL TYPE 3)
 
Authors :  Y. Itoh, S. Chiba, S. Sekine, S. Yokoyama
Date :  18 Jan 10  (Deposition) - 28 Jul 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Rna Complex, Trna, Atp-Binding, Kinase, Nucleotide-Binding, Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chiba, Y. Itoh, S. Sekine, S. Yokoyama
Structural Basis For The Major Role Of O-Phosphoseryl-Trna Kinase In The Uga-Specific Encoding Of Selenocysteine
Mol. Cell V. 39 410 2010
PubMed-ID: 20705242  |  Reference-DOI: 10.1016/J.MOLCEL.2010.07.018

(-) Compounds

Molecule 1 - L-SERYL-TRNA(SEC) KINASE
    Chains: A, B
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD II
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ1538
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM 2661
    Synonym: O-PHOSPHOSERYL-TRNA(SEC) KINASE, PSTK
 
Molecule 2 - SELENOCYSTEINE TRNA
    Chains: C, D
    Engineered: YES
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 2320
    Other Details: TRNASEC WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:9 , GLY A:10 , VAL A:11 , GLY A:12 , LYS A:13 , SER A:14 , THR A:15 , ARG A:112 , ARG A:116 , THR A:150 , HOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1105 , HOH A:1156 , MG A:2003 , G C:37BINDING SITE FOR RESIDUE ANP A 2001
2AC2SOFTWARESER A:14 , HOH A:1001 , HOH A:1002 , HOH A:1003 , ANP A:2001BINDING SITE FOR RESIDUE MG A 2003
3AC3SOFTWARELEU B:8 , PRO B:9 , GLY B:10 , VAL B:11 , GLY B:12 , LYS B:13 , SER B:14 , THR B:15 , ASP B:37 , ARG B:112 , ARG B:116 , THR B:150 , HOH B:1004 , HOH B:1005 , HOH B:1006 , HOH B:1019 , HOH B:1055 , HOH B:1071 , HOH B:1085 , HOH B:1100 , MG B:2004BINDING SITE FOR RESIDUE ANP B 2002
4AC4SOFTWARESER B:14 , HOH B:1004 , HOH B:1005 , HOH B:1006 , ANP B:2002BINDING SITE FOR RESIDUE MG B 2004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ADD)

(-) 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    
   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:251
 aligned with PSTK_METJA | Q58933 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:251
                               1                                                                                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247 
           PSTK_METJA     - ---MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKEFKDLLNSY 248
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhh...eeee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhh.....hhhhhhhhhhhh......hhhhh..eeee.....hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3add A  -2 HHHmLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSmRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKmYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKmEEVDADRVLKEFKDLLNSY 248
                               |     7        17        27        37        47        57        67        77    |   87        97       107       117       127|      137       147       157       167       177       187       197       207       217       227 |     237       247 
                               |                                                                               82-MSE                                       128-MSE                                                                                              229-MSE               
                               1-MSE                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:239
 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.....hhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhh.....hhhhhhhhhhhh......hhhhh..eeee.....hhhhhhhhhhhhhh.....-----------hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3add B  -1 HHmLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSmRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKmYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKF-----------NISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKmEEVDADRVLKEFKDLLNSY 248
                              |      8        18        28        38        48        58        68        78   |    88        98       108       118       128       138       148       158       168    |    -      |188       198       208       218       228|      238       248
                              1-MSE                                                                           82-MSE                                       128-MSE                                      173         185                                         229-MSE               


Chain C from PDB  Type:RNA  Length:88
                                                                                                                        
                 3add C   1 GGCCGCCGCCACCGGGGUGGUCCCCGGGCCGGACGAUCCGGCGCGCCCCGAGUGGGGCGCGGGGUUCAAUUCCCCGCGGCGGCCGCCA  76
                                 ||  8       |19 |      28   ||   42     ||47E||||||||48|       59    || |68        
                                5A|         16|  |          32|        47A||||||47J||||||            64| ||         
                                 5B          18  |           37         47B||||||47K|||||             66 ||         
                                               20A                       47C||||||47L||||              67A|         
                                                                          47D||||| 47M|||               67B         
                                                                           47E||||  47N||                           
                                                                            47F|||    48|                           
                                                                             47G||     50                           
                                                                              47H|                                  
                                                                               47I                                  


Chain D from PDB  Type:RNA  Length:88
                                                                                                                        
                 3add D   1 GGCCGCCGCCACCGGGGUGGUCCCCGGGCCGGACUAGAUCCGGCGCGCCCCGAGUGGGGCGCGGGGUUCAAUUCCCCGCGGCGGCCGC  74
                                 ||  8       |19 |      28    ||  40       47C|||||||47M|||     57      |67A|       
                                5A|         16|  |           33|         47A||||||47J||||||            64| ||       
                                 5B          18  |            36          47B||||||47K|||||             66 ||       
                                               20A                         47C||||||47L||||              67A|       
                                                                            47D||||| 47M|||               67B       
                                                                             47E||||  47N||                         
                                                                              47F|||    48|                         
                                                                               47G||     50                         
                                                                                47H|                                
                                                                                 47I
   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 3ADD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        PSTK_METJA | Q58933: 3a4l 3a4m 3a4n 3adb 3adc 3am1

(-) Related Entries Specified in the PDB File

3adb THE SAME PROTEIN-RNA COMPLEX WITH DIFFERENT CELL PARAMETERS
3adc THE SAME PROTEIN-RNA COMPLEX WITH DIFFERENT CELL PARAMETERS