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(-) Description

Title :  NATIVE STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHASE FROM PSEUDOMONAS AERUGINOSA PA01, WITH BOUND SUBSTRATE MOLECULE GERANYL PYROPHOSPHATE.
 
Authors :  J. W. Schmidberger, R. Schnell, G. Schneider
Date :  07 Feb 13  (Deposition) - 26 Feb 14  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Schmidberger, R. Schnell, G. Schneider
Structural Characterization Of Substrate And Inhibitor Binding To Farnesyl Pyrophosphate Synthase From Pseudomonas Aeruginosa
Acta Crystallogr. , Sect. D V. 71 721 2015
PubMed-ID: 25760619  |  Reference-DOI: 10.1107/S1399004715001121

(-) Compounds

Molecule 1 - GERANYLTRANSTRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET-28 BASED VECTOR
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
    Synonym: PA4043

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2GOL1Ligand/IonGLYCEROL
3GPP2Ligand/IonGERANYL DIPHOSPHATE
4MG5Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:79 , ASP A:83 , ASP A:89 , ARG A:94 , VAL A:154 , GLN A:157 , LYS A:180 , MG A:1296 , MG A:1297 , HOH A:2084 , HOH A:2091 , HOH A:2092 , HOH A:2215 , HOH A:2216 , HOH A:2218BINDING SITE FOR RESIDUE GPP A1295
2AC2SOFTWAREASP A:83 , ASP A:89 , GPP A:1295 , MG A:1297 , HOH A:2084 , HOH A:2092BINDING SITE FOR RESIDUE MG A1296
3AC3SOFTWAREASP A:83 , ASP A:89 , GPP A:1295 , MG A:1296 , HOH A:2082 , HOH A:2083 , HOH A:2091BINDING SITE FOR RESIDUE MG A1297
4AC4SOFTWAREGLN A:221 , VAL A:291 , GLU A:292 , ARG A:293 , ARG A:294BINDING SITE FOR RESIDUE DMS A1298
5AC5SOFTWARESER B:79 , HIS B:82 , ASP B:83 , ASP B:89 , ARG B:94 , GLN B:157 , LYS B:180 , MG B:1293 , MG B:1294 , HOH B:2087 , HOH B:2088 , HOH B:2092 , HOH B:2093 , HOH B:2194 , HOH B:2195 , HOH B:2196BINDING SITE FOR RESIDUE GPP B1292
6AC6SOFTWAREASP B:83 , ASP B:89 , GPP B:1292 , MG B:1294 , HOH B:2088 , HOH B:2093BINDING SITE FOR RESIDUE MG B1293
7AC7SOFTWAREASP B:83 , ASP B:89 , GPP B:1292 , MG B:1293 , HOH B:2086 , HOH B:2087 , HOH B:2092BINDING SITE FOR RESIDUE MG B1294
8AC8SOFTWAREASP B:223 , HOH B:2137 , HOH B:2164 , HOH B:2167 , HOH B:2168 , HOH B:2197BINDING SITE FOR RESIDUE MG B1295
9AC9SOFTWARETYR B:5 , ARG B:8 , ARG B:12 , GLU B:56 , HOH B:2198BINDING SITE FOR RESIDUE GOL B1296

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZMC)

(-) 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:271
 aligned with Q9HWY4_PSEAE | Q9HWY4 from UniProtKB/TrEMBL  Length:295

    Alignment length:294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
         Q9HWY4_PSEAE     1 MIAAYQARCQARVDAALDALFVAPREELQRLYEAMRYSVMNGGKRVRPLLAYAACEALGGAPQRADAAACAVELIHAYSLVHDDLPAMDDDDLRRGQPTTHRAFDEATAILAADGLQALAFEVLADTRRNPQEHAVCLEMLTRLARAAGSAGMVGGQAIDLGSVGVALDQAALEVMHRHKTGALIEASVRLGALASGRAEPASLAALERYAEAIGLAFQVQDDILDVESDTATLGKTQGKDQAHNKPTYPALLGLEAAKGYALELRDLALAALDGFPPSADPLRQLARYIVERR 294
               SCOP domains d3zmca_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.----.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------------.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zmc A   1 MIAAYQARCQARVDAALDALFVAPREELQRLYEAMRYSVMNGGKRVRPLLAYAACEALGGAPQRADAAACAVELIHAYSLVHDDLPAMDDDDLRRGQPTTHRAFDEATAILAADGLQALAFEVLADTRRNPQEHAVCLEMLTRLARAAGSAGMVGGQAIDLGS----LDQAALEVMHRHKTGALIEASVRLGALASGRAEPASLAALERYAEAIGLAFQVQDDILDV-------------------PTYPALLGLEAAKGYALELRDLALAALDGFPPSADPLRQLARYIVERR 294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  |    170       180       190       200       210       220      |  -         -      |250       260       270       280       290    
                                                                                                                                                                                            163  168                                                        227                 247                                               


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with Q9HWY4_PSEAE | Q9HWY4 from UniProtKB/TrEMBL  Length:295

    Alignment length:292
                             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       269       279       289  
         Q9HWY4_PSEAE     - -MIAAYQARCQARVDAALDALFVAPREELQRLYEAMRYSVMNGGKRVRPLLAYAACEALGGAPQRADAAACAVELIHAYSLVHDDLPAMDDDDLRRGQPTTHRAFDEATAILAADGLQALAFEVLADTRRNPQEHAVCLEMLTRLARAAGSAGMVGGQAIDLGSVGVALDQAALEVMHRHKTGALIEASVRLGALASGRAEPASLAALERYAEAIGLAFQVQDDILDVESDTATLGKTQGKDQAHNKPTYPALLGLEAAKGYALELRDLALAALDGFPPSADPLRQLARYIV 291
               SCOP domains d3zmcb_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------------.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zmc B   0 SMIAAYQARCQARVDAALDALFVAPREELQRLYEAMRYSVMNGGKRVRPLLAYAACEALGGAPQRADAAACAVELIHAYSLVHDDLPAMDDDDLRRGQPTTHRAFDEATAILAADGLQALAFEVLADTRRNPQEHAVCLEMLTRLARAAGSAGMVGGQAIDLGSVGVALDQAALEVMHRHKTGALIEASVRLGALASGRAEPASLAALERYAEAIGLAFQVQDDILDV-------------------PTYPALLGLEAAKGYALELRDLALAALDGFPPSADPLRQLARYIV 291
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       | -         -       249       259       269       279       289  
                                                                                                                                                                                                                                                             227                 247
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9HWY4_PSEAE | Q9HWY4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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        Q9HWY4_PSEAE | Q9HWY4: 3zcd 3zl6 3zmb 3zou 4umj

(-) Related Entries Specified in the PDB File

3zmb NATIVE STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHASE FROM PSEUDOMONAS AERUGINOSA PA01, WITH BOUND FRAGMENT SPB02696