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(-) Description

Title :  CRYSTAL STRUCTURE OF GERANYLGERANYL PYROPHOSPHATE SYNTHASE FROM CORYNEBACTERIUM GLUTAMICUM COMPLEXED WITH ISOPRENYL DIPHOSPHATE AND MAGNESIUM
 
Authors :  Y. Patskovsky, R. Toro, J. M. Sauder, C. D. Poulter, J. A. Gerlt, S. K. Bur S. C. Almo, Enzyme Function Initiative (Efi), New York Sgx Rese Center For Structural Genomics (Nysgxrc)
Date :  16 Feb 11  (Deposition) - 02 Mar 11  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Protein Structure Initiative, Geranylgeranyl Pyrophosphate Synthase, Isoprene Biosynthesis, Transferase, New York Sgx Research Center For Structural Genomics, Nysgxrc, Enzyme Function Initiative, Efi, Psi-2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. H. Wallrapp, J. J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson, C. D. Poulter
Prediction Of Function For The Polyprenyl Transferase Subgroup In The Isoprenoid Synthase Superfamily.
Proc. Natl. Acad. Sci. Usa V. 110 E1196 2013
PubMed-ID: 23493556  |  Reference-DOI: 10.1073/PNAS.1300632110

(-) Compounds

Molecule 1 - GERANYLGERANYL PYROPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGL2172
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Strain: ATCC 13032

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1DMA2Ligand/IonDIMETHYLALLYL DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4MSE3Mod. Amino AcidSELENOMETHIONINE
5UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1DMA4Ligand/IonDIMETHYLALLYL DIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4MSE6Mod. Amino AcidSELENOMETHIONINE
5UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:108 , ASP A:112 , ASP A:194 , MG A:382 , DMA A:384 , HOH A:398 , HOH A:399BINDING SITE FOR RESIDUE MG A 381
2AC2SOFTWAREASP A:108 , ASP A:112 , LYS A:271 , MG A:381 , DMA A:384 , HOH A:438 , HOH A:439BINDING SITE FOR RESIDUE MG A 382
3AC3SOFTWAREGLY A:62 , LYS A:63 , ILE A:65 , ARG A:66 , GLN A:101 , ARG A:118 , GLN A:254 , DMA A:384 , HOH A:400 , HOH A:433 , HOH A:449 , HOH A:463 , HOH A:464BINDING SITE FOR RESIDUE DMA A 383
4AC4SOFTWAREALA A:104 , ASP A:108 , ASP A:112 , ARG A:117 , VAL A:187 , GLN A:191 , LYS A:215 , LYS A:271 , LYS A:281 , MG A:381 , MG A:382 , DMA A:383 , HOH A:399 , HOH A:431 , HOH A:432 , HOH A:438 , HOH A:439BINDING SITE FOR RESIDUE DMA A 384
5AC5SOFTWARESER A:84 , GLU A:85 , GLU A:171 , ARG A:175 , HOH A:469BINDING SITE FOR RESIDUE GOL A 386

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QQV)

(-) 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:357
 aligned with Q8NNM1_CORGL | Q8NNM1 from UniProtKB/TrEMBL  Length:371

    Alignment length:357
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       
         Q8NNM1_CORGL    14 LDLDKFPEVVRDRLTQFLDAQELTIADIGAPVTDAVAHLRSFVLNGGKRIRPLYAWAGFLAAQGHKNSSEKLESVLDAAASLEFIQACALIHDDIIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSILAGDMALVWAEDMLQDSGLSAEALARTRDAWRGMRTEVIGGQLLDIYLESHANESVELADSVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAITGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTSPEDIAVITEHIRATGAEEEVEQRISQLTESGLAHLDDVDIPDEVRAQLRALAIRSTERR 370
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------polyprenyl_synt-3qqvA01 A:138-328                                                                                                                                                              -------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------polyprenyl_synt-3qqvA02 A:138-328                                                                                                                                                              -------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qqv A  16 LDLDKFPEVVRDRLTQFLDAQELTIADIGAPVTDAVAHLRSFVLNGGKRIRPLYAWAGFLAAQGHKNSSEKLESVLDAAASLEFIQACALIHDDIIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSILAGDmALVWAEDmLQDSGLSAEALARTRDAWRGmRTEVIGGQLLDIYLESHANESVELADSVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAITGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTSPEDIAVITEHIRATGAEEEVEQRISQLTESGLAHLDDVDIPDEVRAQLRALAIRSTERR 372
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155      |165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       
                                                                                                                                                                    154-MSE 162-MSE              183-MSE
   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 3QQV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: polyprenyl_synt] (86)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8NNM1_CORGL | Q8NNM1)
molecular function
    GO:0004161    dimethylallyltranstransferase activity    Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
    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.

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