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(-) Description

Title :  X-RAY STRUCTURES OF ISOPENTENYL PHOSPHATE KINASE
 
Authors :  C. P. Hill, H. L. Schubert
Date :  28 Jan 10  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mevalonate Biosynthesis Isoprenoid, 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 - ISOPENTENYL PHOSPHATE KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)CODON PLUS
    Expression System Taxid: 469008
    Gene: MTH47, MTH_47
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:47 , GLY B:51 , HIS B:52 , ALA B:55 , GLY B:140BINDING SITE FOR RESIDUE GOL B 267
2AC2SOFTWARELYS A:5 , GLY A:7 , GLY A:8 , SER A:9 , THR A:177 , ASP A:178 , VAL A:179 , GLY A:181 , TYR A:183 , ARG A:185 , ASN A:186 , PRO A:187 , LYS A:188 , GLY A:219 , MSE A:220 , HOH A:278 , HOH A:313 , HOH A:317BINDING SITE FOR RESIDUE ADP A 267
3AC3SOFTWAREGLY B:7 , GLY B:8 , SER B:9 , THR B:177 , ASP B:178 , VAL B:179 , GLY B:181 , TYR B:183 , ARG B:185 , ASN B:186 , PRO B:187 , LYS B:188 , MSE B:220 , LYS B:223 , HOH B:273 , HOH B:289 , HOH B:311 , HOH B:316BINDING SITE FOR RESIDUE ADP B 268

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LL9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:219 -Mse A:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LL9)

(-) Exons   (0, 0)

(no "Exon" information available for 3LL9)

(-) 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:244
 aligned with IPK_METTH | O26153 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
            IPK_METTH     - -MIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLMIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSMQPSAFIRAHAGRISHADISLIRSYLEEGMVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLMPERVILGTDVDGVYTRNPKKHPDARLLDVIGSLDDLESLDGTLNTDVTGGMVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRI 262
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhee......eehhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhh.eeee..eeeee.hhhhhhhhhh..eeeee.eeee.......eeeehhhhhhhhhhhhhh..eeeeee......................-------------------..hhhhhhhhhhhhh...eeeee....hhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll9 A  -1 HmIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLmIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSmQPSAFIRAHAGRISHADISLIRSYLEEGmVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLmPERVILGTDVDGVYTRNPKKHPDARLLDVI-------------------GmVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRI 262
                            ||       9        19        29        39  |     49        59        69        79        89        99     | 109       119       129    |  139       149       159       169       179       189       199         -       219|      229       239       249       259   
                            ||                                       42-MSE                                                        105-MSE                      134-MSE                            169-MSE                       199                 219|                                          
                           -1|                                                                                                                                                                                                                        220-MSE                                      
                             1-MSE                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with IPK_METTH | O26153 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:264
                             1                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259    
            IPK_METTH     - -MIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLMIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSMQPSAFIRAHAGRISHADISLIRSYLEEGMVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLMPERVILGTDVDGVYTRNPKKHPDARLLDVIGSLDDLESLDGTLNTDVTGGMVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRIT 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhee......eehhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhh.eeee..eeeee.hhhhhhhhhh..eeeee.eeee.......eeeehhhhhhhhhhhhhh..eeeeee....................ee....---------------hhhhhhhhhhhhhhh...eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ll9 B  -1 HmIILKLGGSVITRKDSEEPAIDRDNLERIASEIGNASPSSLmIVHGAGSFGHPFAGEYRIGSEIENEEDLRRRRFGFALTQNWVKKLNSHVCDALLAEGIPAVSmQPSAFIRAHAGRISHADISLIRSYLEEGmVPVVYGDVVLDSDRRLKFSVISGDQLINHFSLRLmPERVILGTDVDGVYTRNPKKHPDARLLDVIGSLD---------------GmVGKIRELLLLAEKGVESEIINAAVPGNIERALLGEEVRGTRIT 263
                            ||       9        19        29        39  |     49        59        69        79        89        99     | 109       119       129    |  139       149       159       169       179       189       199   |     -       219|      229       239       249       259    
                           -1|                                       42-MSE                                                        105-MSE                      134-MSE                            169-MSE                           203             219|                                           
                             1-MSE                                                                                                                                                                                                                    220-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3LL9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LL9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LL9)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IPK_METTH | O26153)
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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 Related Entries

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(-) Related Entries Specified in the PDB File

3lkk THERMOPLASMA ACIDOPHILUM ISOPENTENYL PHOSPHATE KINASE SUBSTRATE COMPLEX
3ll5 THERMOPLASMA ACIDOPHILUM ISOPENTENYL PHOSPHATE KINASE PRODUCT COMPLEX