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(-) Description

Title :  CRYSTAL STRUCTURE OF T. ACIDOPHILUM ISOPENTENYL PHOSPHATE KINASE PRODUCT COMPLEX
 
Authors :  M. F. Mabanglo, C. P. Hill
Date :  28 Jan 10  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Alternate Mevalonate Pathway, Isopentenyl Phsophate Kinase, Alpha- Beta-Alpha Sandwich Fold, Product 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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 56)

Asymmetric Unit (5, 56)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3IP82Ligand/IonISOPENTENYL PHOSPHATE
4IPE2Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
5MSE48Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (5, 28)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3IP81Ligand/IonISOPENTENYL PHOSPHATE
4IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
5MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (5, 28)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3IP81Ligand/IonISOPENTENYL PHOSPHATE
4IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
5MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:5 , GLY A:7 , GLY A:8 , SER A:9 , LYS A:14 , THR A:163 , ASP A:164 , GLY A:167 , TYR A:169 , ASP A:172 , PRO A:173 , LYS A:174 , ILE A:202 , LYS A:205 , IPE A:247 , HOH A:251 , HOH A:299BINDING SITE FOR RESIDUE ADP A 246
2AC2SOFTWARELYS A:5 , GLY A:8 , LYS A:14 , GLY A:44 , GLY A:45 , GLY A:46 , GLY A:49 , HIS A:50 , GLY A:128 , SER A:142 , GLY A:143 , ADP A:246 , HOH A:291 , HOH A:306BINDING SITE FOR RESIDUE IPE A 247
3AC3SOFTWAREGLU A:237 , LYS B:5 , GLY B:7 , GLY B:8 , SER B:9 , LYS B:14 , THR B:163 , ASP B:164 , GLY B:167 , TYR B:169 , LYS B:171 , ASP B:172 , LYS B:174 , GLY B:201 , ILE B:202 , LYS B:205 , IPE B:247 , HOH B:250 , HOH B:284BINDING SITE FOR RESIDUE ADP B 246
4AC4SOFTWARELYS B:5 , GLY B:8 , LYS B:14 , GLY B:44 , GLY B:45 , GLY B:46 , GLY B:49 , HIS B:50 , GLY B:128 , ILE B:140 , SER B:142 , GLY B:143 , ADP B:246 , HOH B:272 , HOH B:290BINDING SITE FOR RESIDUE IPE B 247
5AC5SOFTWARELYS C:5 , GLY C:7 , GLY C:8 , SER C:9 , GLY C:44 , GLY C:46 , HIS C:50 , ASP C:164 , GLY C:167 , TYR C:169 , LYS C:171 , ASP C:172 , PRO C:173 , LYS C:174 , GLY C:201 , ILE C:202 , LYS C:205 , IP8 C:247 , HOH C:264 , HOH C:269 , HOH C:297BINDING SITE FOR RESIDUE ATP C 246
6AC6SOFTWARELYS C:5 , GLY C:44 , GLY C:45 , GLY C:46 , HIS C:50 , GLY C:143 , ATP C:246 , HOH C:271 , HOH C:275 , HOH C:279 , HOH C:311BINDING SITE FOR RESIDUE IP8 C 247
7AC7SOFTWARELYS D:5 , GLY D:7 , GLY D:8 , SER D:9 , GLY D:44 , GLY D:46 , HIS D:50 , ASP D:164 , GLY D:167 , TYR D:169 , LYS D:171 , ASP D:172 , PRO D:173 , LYS D:174 , ILE D:202 , LYS D:205 , IP8 D:247 , HOH D:279 , HOH D:284 , HOH D:285BINDING SITE FOR RESIDUE ATP D 246
8AC8SOFTWARELYS D:5 , GLY D:44 , GLY D:45 , GLY D:46 , GLY D:49 , HIS D:50 , GLY D:128 , ATP D:246 , HOH D:262 , HOH D:263 , HOH D:272 , HOH D:281 , HOH D:293BINDING SITE FOR RESIDUE IP8 D 247

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LL5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:58 -Pro A:59
2Leu B:58 -Pro B:59
3Leu C:58 -Pro C:59
4Leu D:58 -Pro D:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LL5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LL5)

(-) Exons   (0, 0)

(no "Exon" information available for 3LL5)

(-) 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:233
 aligned with IPK_THEAC | Q9HLX1 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:246
                             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      
            IPK_THEAC     - -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....................eee..-------------hhhhhhhhhhhhh.....eeeee..hhhhhhhh.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ll5 A   0 TmmILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAmEFGLPGPKNPRSSIGYSIVHRDmENLDLmVIDAmIEmGmRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDImADmAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTN-------------IGKKFESmVKmKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
                             ||      9        19        29        39        49    |   59        69       |79   |    89 | |    99       109       119       129       139       149|      159       169       179        |-         -  |    209  |    219       229       239      
                             ||                                                  54-MSE                 77-MSE |    |  | |                                                   147-MSE                                  188           202      |  |                                 
                             1-MSE                                                                            83-MSE|  | |                                                      150-MSE                                                    209-MSE                                
                              2-MSE                                                                                88-MSE|                                                                                                                    212-MSE                             
                                                                                                                      91-MSE                                                                                                                                                      
                                                                                                                        93-MSE                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with IPK_THEAC | Q9HLX1 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:246
                             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      
            IPK_THEAC     - -MMILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAMEFGLPGPKNPRSSIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDIMADMAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTNITFDRVQNDVTGGIGKKFESMVKMKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhh........hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhh.......hhhhhhhhhhh.eeeee.eeeeee..eeeeehhhhhhhhhhhhhh..eeeeee....................ee...------------hhhhhhhhhhhhh......eeeee..hhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ll5 B   0 TmmILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAmEFGLPGPKNPRSSIGYSIVHRDmENLDLmVIDAmIEmGmRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDImADmAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTN------------GIGKKFESmVKmKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
                             ||      9        19        29        39        49    |   59        69       |79   |    89 | |    99       109       119       129       139       149|      159       169       179        |-         - |     209  |    219       229       239      
                             1-MSE                                               54-MSE                 77-MSE |    |  | |                                                   147-MSE                                  188          201     209-MSE                                
                              2-MSE                                                                           83-MSE|  | |                                                      150-MSE                                                       212-MSE                             
                                                                                                                   88-MSE|                                                                                                                                                        
                                                                                                                      91-MSE                                                                                                                                                      
                                                                                                                        93-MSE                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with IPK_THEAC | Q9HLX1 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:249
                                1                                                                                                                                                                                                                                                    
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236         
            IPK_THEAC     - ----MMILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAMEFGLPGPKNPRSSIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDIMADMAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTNITFDRVQNDVTGGIGKKFESMVKMKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhh........hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhh.......hhhhhhhhhh..eeeee.eeeeee..eeeeehhhhhhhhhhhhhh..eeeeee....................eee..------------.hhhhhhhhhhhhhh....eeeee..hhhhhhhh.......eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll5 C  -3 DPFTmmILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAmEFGLPGPKNPRSSIGYSIVHRDmENLDLmVIDAmIEmGmRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDImADmAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTN------------GIGKKFESmVKmKSSVKNGVYLINGNHPERIGDIGKESFIGTVIR 245
                                ||   6        16        26        36        46       |56        66        76|     | 86 |  | | 96       106       116       126       136       146|  |   156       166       176       186 |       -    |  206  |  | 216       226       236         
                                1-MSE                                               54-MSE                 77-MSE |    |  | |                                                   147-MSE                                  188          201     209-MSE                                
                                 2-MSE                                                                           83-MSE|  | |                                                      150-MSE                                                       212-MSE                             
                                                                                                                      88-MSE|                                                                                                                                                        
                                                                                                                         91-MSE                                                                                                                                                      
                                                                                                                           93-MSE                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:234
 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........hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhh.......hhhhhhhhhh..eeeee.eeeeee..eeeeehhhhhhhhhhhhhh..eeeeee.........................-------------hhhhhhhhhhhhhhh...eeeee..hhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll5 D  -1 FTmmILKIGGSVITDKSAYRTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKAmEFGLPGPKNPRSSIGYSIVHRDmENLDLmVIDAmIEmGmRPISVPISALRYDGRFDYTPLIRYIDAGFVPVSYGDVYIKDEHSYGIYSGDDImADmAELLKPDVAVFLTDVDGIYSKDPKRNPDAVLLRDIDTN-------------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       
                              1-MSE                                               54-MSE                 77-MSE |    |  | |                                                   147-MSE                                  188           202      |  |                                 
                               2-MSE                                                                           83-MSE|  | |                                                      150-MSE                                                    209-MSE                                
                                                                                                                    88-MSE|                                                                                                                    212-MSE                             
                                                                                                                       91-MSE                                                                                                                                                      
                                                                                                                         93-MSE
   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 3LL5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LL5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LL5)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        IPK_THEAC | Q9HLX1: 3lkk

(-) Related Entries Specified in the PDB File

3lkk T. ACIDOPHILUM ISOPENTENYL PHOSPHATE KINASE PRODUCT COMPLEX
3ll9