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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEOGLOBUS FULGIDUS RIO1 KINASE BOUND TO TOYOCAMYCIN.
 
Authors :  I. N. Kiburu, N. Laronde-Leblanc
Date :  02 Apr 11  (Deposition) - 09 May 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Atypical Kinase, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. N. Kiburu, N. Laronde-Leblanc
Interaction Of Rio1 Kinase With Toyocamycin Reveals A Conformational Switch That Controls Oligomeric State And Catalytic Activity.
Plos One V. 7 37371 2012
PubMed-ID: 22629386  |  Reference-DOI: 10.1371/JOURNAL.PONE.0037371

(-) Compounds

Molecule 1 - RIO-TYPE SERINE/THREONINE-PROTEIN KINASE RIO1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST527
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIO1, AF_1804
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: AFRIO1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1TO12Ligand/Ion4-AMINO-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TO11Ligand/Ion4-AMINO-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TO11Ligand/Ion4-AMINO-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:55 , SER A:56 , ALA A:78 , PRO A:135 , MET A:147 , GLU A:148 , PHE A:149 , ILE A:150 , PRO A:156 , THR A:159 , ILE A:211 , ASP A:212 , HOH A:263 , HOH A:275 , HOH A:279 , HOH A:342BINDING SITE FOR RESIDUE TO1 A 259
2AC2SOFTWAREILE B:55 , SER B:56 , ALA B:78 , PRO B:135 , MET B:147 , GLU B:148 , PHE B:149 , ILE B:150 , PRO B:156 , ILE B:211 , ASP B:212 , HOH B:268 , HOH B:279 , HOH B:295 , HOH B:298BINDING SITE FOR RESIDUE TO1 B 259

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RE4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RE4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RE4)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIO1PS01245 RIO1/ZK632.3/MJ0444 family signature.RIO1_ARCFU192-203
 		  2A:192-203
B:192-203
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIO1PS01245 RIO1/ZK632.3/MJ0444 family signature.RIO1_ARCFU192-203
 		  1A:192-203
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIO1PS01245 RIO1/ZK632.3/MJ0444 family signature.RIO1_ARCFU192-203
 		  1-
B:192-203

(-) Exons   (0, 0)

(no "Exon" information available for 3RE4)

(-) 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:252
 aligned with RIO1_ARCFU | O28471 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      
           RIO1_ARCFU     3 DLKKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAMGGVISTGKEANVFYADGVFDGKPVAMAVKIYRIETSEFDKMDEYLYGDERFDMRRISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYMKNVLLMEFIGEDELPAPTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNIMYIDKVYFIDMGQAVTLRHPMAESYLERDVRNIIRFFSKYGVKADFEEMLKEVKGE 258
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee...----hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeee..ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eee...eee......ee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIO1        ------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re4 A   3 DLKKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAMGGVISTGKEANVFYADGVFDGKPVAMAVKIYRIE----DKMDEYLYGDERFDMRRISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYMKNVLLMEFIGEDELPAPTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNIMYIDKVYFIDMGQAVTLRHPMAESYLERDVRNIIRFFSKYGVKADFEEMLKEVKGE 258
                                    12        22        32        42        52        62        72        82  |    |92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      
                                                                                                             85   90                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with RIO1_ARCFU | O28471 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      
           RIO1_ARCFU     3 DLKKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAMGGVISTGKEANVFYADGVFDGKPVAMAVKIYRIETSEFDKMDEYLYGDERFDMRRISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYMKNVLLMEFIGEDELPAPTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNIMYIDKVYFIDMGQAVTLRHPMAESYLERDVRNIIRFFSKYGVKADFEEMLKEVKGE 258
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee...-------......hhhhh.......hhhhhhhhhhhhhhhhhhhh......eeeee..eeeee..ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eee...eee......ee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIO1        ------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re4 B   3 DLKKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAMGGVISTGKEANVFYADGVFDGKPVAMAVKIYRIE-------DEYLYGDERFDMRRISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYMKNVLLMEFIGEDELPAPTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNIMYIDKVYFIDMGQAVTLRHPMAESYLERDVRNIIRFFSKYGVKADFEEMLKEVKGE 258
                                    12        22        32        42        52        62        72        82  |      -|      102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      
                                                                                                             85      93
   Legend:   → Mismatch (orange background)
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  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 3RE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RE4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1ztf 1zth 4jin

(-) Related Entries Specified in the PDB File

1zp9 CRYSTAL STRUCTURE OF FULL-LEGNTH A.FULGIDUS RIO1 SERINE KINASE BOUND TO ATP AND MN2+ IONS.
1ztf CRYSTAL STRUCTURE OF A.FULGIDUS RIO1 SERINE PROTEIN KINASE
1zth CRYSTAL STRUCTURE OF A.FULGIDUS RIO1 SERINE PROTEIN KINASE BOUND TO ADP AND MANGANESE ION