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(-) Description

Title :  CRYSTAL STRUCTURE OF A.FULGIDUS RIO1 SERINE PROTEIN KINASE
 
Authors :  A. Wlodawer, N. Laronde-Leblanc
Date :  26 May 05  (Deposition) - 19 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase, Ribosome Biogenesis, Rrna, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Laronde-Leblanc, T. Guszczynski, T. Copeland, A. Wlodawer
Structure And Activity Of The Atypical Serine Kinase Rio1.
Febs J. V. 272 3698 2005
PubMed-ID: 16008568  |  Reference-DOI: 10.1111/J.1742-4658.2005.04796.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIO1 SERINE PROTEIN KINASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIO1
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2XYA1Ligand/Ion2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:55 , SER A:56 , PRO A:135 , GLU A:148 , PHE A:149 , ILE A:150 , MSE A:203 , ILE A:211 , HOH A:309 , HOH A:332 , HOH A:410BINDING SITE FOR RESIDUE XYA A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIO1PS01245 RIO1/ZK632.3/MJ0444 family signature.RIO1_ARCFU192-203  1A:192-203

(-) Exons   (0, 0)

(no "Exon" information available for 1ZTF)

(-) 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:253
 aligned with RIO1_ARCFU | O28471 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:253
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254   
           RIO1_ARCFU     5 KKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAMGGVISTGKEANVFYADGVFDGKPVAMAVKIYRIETSEFDKMDEYLYGDERFDMRRISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYMKNVLLMEFIGEDELPAPTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNIMYIDKVYFIDMGQAVTLRHPMAESYLERDVRNIIRFFSKYGVKADFEEMLKEVKG 257
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------RIO1-1ztfA01 A:62-251                                                                                                                                                                         ------ Pfam domains
         Sec.struct. author .....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee..eeeeeeeeee.......hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeee..ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eee...eee.hhh.eee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIO1        ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ztf A   5 KKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAmGGVISTGKEANVFYADGVFDGKPVAmAVKIYRIETSEFDKmDEYLYGDERFDmRRISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYmKNVLLmEFIGEDELPAPTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNImYIDKVYFIDmGQAVTLRHPmAESYLERDVRNIIRFFSKYGVKADFEEmLKEVKG 257
                                    14        24        34        44      | 54        64        74  |     84       |94       104       114       124       134      |144  |    154       164       174       184       194       204       214       224       234       244      |254   
                                                                         51-MSE                    77-MSE         92-MSE     104-MSE                              141-MSE |                                                     203-MSE   213-MSE   223-MSE                     251-MSE  
                                                                                                                                                                        147-MSE
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  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 1ZTF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIO1_ARCFU | O28471)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIO1_ARCFU | O28471: 1zp9 1zth 3re4 4jin

(-) Related Entries Specified in the PDB File

1zp9 CRYSTAL STRUCTURE OF A.FULGIDUS RIO1 BOUND TO ATP AND MANGANESE ION.