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(-) Description

Title :  CRYSTAL STRUCTURE OF ISOPRENOID SYNTHASE A3MSH1 (TARGET EFI-501992) FROM PYROBACULUM CALIDIFONTIS COMPLEXED WITH DMAPP AND MAGNESIUM
 
Authors :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H C. D. Poulter, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (
Date :  20 Aug 12  (Deposition) - 10 Oct 12  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isoprenoid Synthesis, Isoprenoid Diphosphate Synthase, Geranylgeranyl Diphosphate Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, C. D. Poulter, J. A. Gerlt, S. C. Almo
Crystal Structure Of Isoprenoid Synthase From Pyrobaculum Calidifontis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYPRENYL SYNTHETASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PCAL_0150
    Organism Scientific: PYROBACULUM CALIDIFONTIS
    Organism Taxid: 410359
    Strain: JCM 11548/VA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1DMA4Ligand/IonDIMETHYLALLYL DIPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:85 , ASP A:89 , MG A:402 , DMA A:403 , HOH A:561 , HOH A:591BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREASP A:85 , ASP A:89 , MG A:401 , DMA A:403 , HOH A:574 , HOH A:584 , HOH A:585BINDING SITE FOR RESIDUE MG A 402
03AC3SOFTWARESER A:81 , LEU A:82 , ASP A:85 , ASP A:89 , ARG A:94 , LYS A:249 , MG A:401 , MG A:402 , DMA A:404 , HOH A:561 , HOH A:584 , HOH A:585 , HOH A:591 , HOH A:632BINDING SITE FOR RESIDUE DMA A 403
04AC4SOFTWAREGLY A:45 , LYS A:46 , ARG A:49 , HIS A:78 , ARG A:95 , THR A:185 , GLN A:222 , DMA A:403 , HOH A:507 , HOH A:510 , HOH A:546 , HOH A:586 , HOH A:613BINDING SITE FOR RESIDUE DMA A 404
05AC5SOFTWAREASP A:225 , ASP A:229 , HOH A:543 , HOH A:575 , HOH A:582 , HOH A:594BINDING SITE FOR RESIDUE MG A 405
06AC6SOFTWAREASP B:85 , ASP B:89 , MG B:402 , DMA B:404 , HOH B:565 , HOH B:566 , HOH B:567BINDING SITE FOR RESIDUE MG B 401
07AC7SOFTWAREASP B:85 , ASP B:89 , MG B:401 , DMA B:404 , HOH B:564 , HOH B:593BINDING SITE FOR RESIDUE MG B 402
08AC8SOFTWAREASP B:225 , ASP B:229 , HOH B:544 , HOH B:574 , HOH B:575 , HOH B:576BINDING SITE FOR RESIDUE MG B 403
09AC9SOFTWARESER B:81 , LEU B:82 , ASP B:85 , ASP B:89 , ARG B:94 , LYS B:184 , LYS B:243 , LYS B:249 , MG B:401 , MG B:402 , HOH B:564 , HOH B:566 , HOH B:567 , HOH B:593BINDING SITE FOR RESIDUE DMA B 404
10BC1SOFTWARELYS B:46 , ARG B:49 , HIS B:78 , ARG B:95 , THR B:185 , PHE B:221 , HOH B:505 , HOH B:559 , HOH B:568 , HOH B:594BINDING SITE FOR RESIDUE DMA B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GP2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GP2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GP2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GP2)

(-) Exons   (0, 0)

(no "Exon" information available for 4GP2)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gp2 A   3 MDVVSRLHQKYGAEVEKALVRYLSIGLAEDFREAVLYQVKTGGKRLRPLLTLAAAEAVSGQWRPALPAAAIVELIHNYSLIYDDIIDRGDVRRGLPTVRKAFGDNAAILVGIWYREAIEEAVLDTPKPTLFAKEVAEVIKAIDEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKMVSLKTGALIAAAAKWGVLSVSDDRGLAEAAWNFGMAAGVAFQIIDDVLDIYGDPKKFGKEIGKDIKEHKRGNAVVAVALSHLGEGERRRLLEILAREVVEEADVREAVALLDSVGAREEALRLAARYREEAERHLAKIPNNGTLKELLDFIVAREYAENLYFQS 344
                                    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       262       272       282       292       302       312       322       332       342  


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gp2 B   4 DVVSRLHQKYGAEVEKALVRYLSIGLAEDFREAVLYQVKTGGKRLRPLLTLAAAEAVSGQWRPALPAAAIVELIHNYSLIYDDIIDRGDVRRGLPTVRKAFGDNAAILVGIWYREAIEEAVLDTPKPTLFAKEVAEVIKAIDEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKMVSLKTGALIAAAAKWGVLSVSDDRGLAEAAWNFGMAAGVAFQIIDDVLDIYGDEIGKDIKEHKRGNAVVAVALSHLGEGERRRLLEILAREVVEEADVREAVALLDSVGAREEALRLAARYREEAERHLAKIPNNGTLKELLDFIVAREYAENL 340
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233|      249       259       269       279       289       299       309       319       329       339 
                                                                                                                                                                                                                                                               233|                                                                                                    
                                                                                                                                                                                                                                                                240
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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 4GP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GP2)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        A3MSH1_PYRCJ | A3MSH1: 4dhd 4gp1

(-) Related Entries Specified in the PDB File

4dhd UN-LIGANDED STRUCTURE
4gp1 COMPLEX WITH DMAPP LIGAND