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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ISOPENTENYL PHOSPHATE KINASE SUBSTRATE COMPLEX
 
Authors :  M. F. Mabanglo, C. P. Hill
Date :  27 Jan 10  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isopentenyl Phosphate Kinase, Alternate Mevalonate Pathway, Alpha- Beta-Alpha Sandwich Fold, Substrate Complex, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Mabanglo, H. L. Schubert, M. Chen, C. P. Hill, C. D. Poulter
X-Ray Structures Of Isopentenyl Phosphate Kinase.
Acs Chem. Biol. V. 5 517 2010
PubMed-ID: 20402538  |  Reference-DOI: 10.1021/CB100032G

(-) Compounds

Molecule 1 - GAMMA-GLUTAMYL KINASE RELATED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D-TOPO
    Expression System Strain: BL21(DE3) CODON PLUS RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TA0103
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 273075
    Strain: DSM1728
    Synonym: ISOPENTENYL PHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2IP82Ligand/IonISOPENTENYL PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:5 , GLY A:7 , GLY A:8 , SER A:9 , LYS A:14 , GLY A:44 , GLY A:45 , GLY A:46 , HIS A:50 , ASP A:164 , GLY A:167 , TYR A:169 , LYS A:171 , ASP A:172 , PRO A:173 , LYS A:174 , LYS A:205 , IP8 A:247 , HOH A:287 , HOH A:357 , HOH A:361BINDING SITE FOR RESIDUE ATP A 246
2AC2SOFTWARELYS A:5 , GLY A:44 , GLY A:45 , GLY A:49 , HIS A:50 , GLY A:128 , SER A:142 , GLY A:143 , ATP A:246 , HOH A:292BINDING SITE FOR RESIDUE IP8 A 247
3AC3SOFTWARELYS B:5 , GLY B:7 , GLY B:8 , SER B:9 , LYS B:14 , GLY B:44 , GLY B:45 , GLY B:46 , HIS B:50 , ASP B:164 , VAL B:165 , GLY B:167 , TYR B:169 , LYS B:171 , ASP B:172 , PRO B:173 , LYS B:174 , ILE B:202 , LYS B:205 , IP8 B:247 , HOH B:272 , HOH B:330BINDING SITE FOR RESIDUE ATP B 246
4AC4SOFTWARELYS B:5 , GLY B:44 , GLY B:45 , GLY B:49 , HIS B:50 , GLY B:128 , ASP B:129 , SER B:142 , GLY B:143 , ATP B:246BINDING SITE FOR RESIDUE IP8 B 247

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:58 -Pro A:59
2Leu B:58 -Pro B:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LKK)

(-) 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:232
 aligned with IPK_THEAC | Q9HLX1 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            IPK_THEAC     1 MMILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAMEFGLPGPKNPRSSIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDIMADMAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTNITFDRVQNDVTGGIGKKFESMVKMKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhh........hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhh.......hhhhhhhhhh..eeeee.eeeeee..eeeeehhhhhhhhhhhhhh..eeeeee....................ee...-------------hhhhhhhhhhhhhhh...eeeee..hhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lkk A   1 MMILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAMEFGLPGPKNPRSSIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDIMADMAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTN-------------IGKKFESMVKMKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -         - |     210       220       230       240     
                                                                                                                                                                                                                     188           202                                           


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with IPK_THEAC | Q9HLX1 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:247
                              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       
            IPK_THEAC     - --MMILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAMEFGLPGPKNPRSSIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDIMADMAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTNITFDRVQNDVTGGIGKKFESMVKMKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhh........hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhh.......hhhhhhhhhh..eeeee.eeeeee..eeeeehhhhhhhhhhhhhh..eeeeee....................eee......---------hhhhhhhhhhhh......eeeee..hhhhhhhh.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lkk B  -1 FTMMILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAMEFGLPGPKNPRSSIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDIMADMAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTNITFD---------IGKKFESMVKMKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   |     -   |   208       218       228       238       
                                                                                                                                                                                                                           192       202
   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 3LKK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IPK_THEAC | Q9HLX1)
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: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:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    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.

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        IPK_THEAC | Q9HLX1: 3ll5

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