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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BIFUNCTIONAL CHORISMATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  S. Quevillon-Cheruel, N. Leulliot, P. Meyer, M. Graille, M. Bremang, K. Blondeau, I. Sorel, A. Poupon, J. Janin, H. Van Tilbeurgh
Date :  09 Oct 03  (Deposition) - 23 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Two Layers Alpha-Beta, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Quevillon-Cheruel, N. Leulliot, P. Meyer, M. Graille, M. Bremang, K. Blondeau, I. Sorel, A. Poupon, J. Janin, H. Van Tilbeurgh
Crystal Structure Of The Bifunctional Chorismate Synthase From Saccharomyces Cerevisiae
J. Biol. Chem. V. 279 619 2004
PubMed-ID: 14573601  |  Reference-DOI: 10.1074/JBC.M310380200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHORISMATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YGL148W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: 5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE PHOSPHOLYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1R52)

(-) Sites  (0, 0)

(no "Site" information available for 1R52)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R52)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:339 -Pro A:340
2Asp B:339 -Pro B:340
3Asp C:339 -Pro C:340
4Asp D:339 -Pro D:340

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R52)

(-) PROSITE Motifs  (3, 12)

Asymmetric/Biological Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHORISMATE_SYNTHASE_1PS00787 Chorismate synthase signature 1.AROC_YEAST14-29
 
 
 		  4A:14-29
B:14-29
C:14-29
D:14-29
2CHORISMATE_SYNTHASE_2PS00788 Chorismate synthase signature 2.AROC_YEAST122-138
 
 
 		  4A:128-138
B:127-138
C:127-138
D:127-138
3CHORISMATE_SYNTHASE_3PS00789 Chorismate synthase signature 3.AROC_YEAST337-353
 
 
 		  4A:337-353
B:337-353
C:337-353
D:337-353

(-) Exons   (1, 4)

Asymmetric/Biological Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL148W1YGL148W.1VII:226404-2275341131AROC_YEAST1-3763764A:1-370 (gaps)
B:1-370 (gaps)
C:1-370 (gaps)
D:1-370 (gaps)		370
370
370
370

(-) 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:283
 aligned with AROC_YEAST | P28777 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:370
                                    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       300       310       320       330       340       350       360       370
           AROC_YEAST     1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKDRVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGGGRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNGENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
               SCOP domains d1r52a_ A: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeeee......eeeeee....eee.hhhhhhhhhhh..-------------..eee.......ee....eeeee.-------------------------------------------.hhhhhhhhhhhhhhhhhh...eeeeeeeee..ee......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeee............hhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh....--------........ee..ee....eeeeeee...-----------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA----------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-370 (gaps) UniProt: 1-376 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                          Transcript 1
                 1r52 A   1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRR-------------DRVEIQSGTEFGKTLGTPIAMMIK-------------------------------------------ETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYF--------TKTNNSGGVQGGISNGENIYFSVPFKSV-----------------------RHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
                                    10        20        30        40      |  -         -|       70        80   |     -         -         -         -       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      |  -     | 290       300       310  |      -         -      |340       350       360       370
                                                                         47            61                     84                                         128                                                                                                                                                  277      286                        313                     337                                 


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with AROC_YEAST | P28777 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:370
                                    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       300       310       320       330       340       350       360       370
           AROC_YEAST     1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKDRVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGGGRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNGENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
               SCOP domains d1r52b_ B: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee.......eeeeee....eee.hhhhhhhhhhh..--------------.eee...ee..ee....eeeee.------------------------------------------..hhhhhhhhhhhhhhhhhh...eeeeeeeee..ee......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeee............hhhhhhhhhhhh.....eeee...hhhhh.hhhhhhh...---------........ee..ee....eeeeeee...-----------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA----------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-370 (gaps) UniProt: 1-376 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                          Transcript 1
                 1r52 B   1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRR--------------RVEIQSGTEFGKTLGTPIAMMIK------------------------------------------RETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFY---------TKTNNSGGVQGGISNGENIYFSVPFKSV-----------------------RHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
                                    10        20        30        40      |  -         - |      70        80   |     -         -         -         -      |130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     |   -     | 290       300       310  |      -         -      |340       350       360       370
                                                                         47             62                    84                                        127                                                                                                                                                  276       286                        313                     337                                 


Chain C from PDB  Type:PROTEIN  Length:283
 aligned with AROC_YEAST | P28777 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:370
                                    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       300       310       320       330       340       350       360       370
           AROC_YEAST     1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKDRVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGGGRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNGENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
               SCOP domains d1r52c_ C: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeeee......eeeeee....eee.hhhhhhhhhhh..-------------..eee...ee..ee....eeeee.------------------------------------------..hhhhhhhhhhhhhhhhhh...eeeeeeeee..ee......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeee............hhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh...---------........ee..ee....eeeeeee...-----------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA----------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-370 (gaps) UniProt: 1-376 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                          Transcript 1
                 1r52 C   1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRR-------------DRVEIQSGTEFGKTLGTPIAMMIK------------------------------------------RETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFY---------TKTNNSGGVQGGISNGENIYFSVPFKSV-----------------------RHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
                                    10        20        30        40      |  -         -|       70        80   |     -         -         -         -      |130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     |   -     | 290       300       310  |      -         -      |340       350       360       370
                                                                         47            61                     84                                        127                                                                                                                                                  276       286                        313                     337                                 


Chain D from PDB  Type:PROTEIN  Length:282
 aligned with AROC_YEAST | P28777 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:370
                                    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       300       310       320       330       340       350       360       370
           AROC_YEAST     1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKDRVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGGGRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNGENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
               SCOP domains d1r52d_ D: Chorismate synthase, AroC                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Chorismate_synt-1r52D01 D:8-364                                                                                                                                                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -------Chorismate_synt-1r52D02 D:8-364                                                                                                                                                                                                                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) -------Chorismate_synt-1r52D03 D:8-364                                                                                                                                                                                                                                                                                                                                      ------ Pfam domains (3)
           Pfam domains (4) -------Chorismate_synt-1r52D04 D:8-364                                                                                                                                                                                                                                                                                                                                      ------ Pfam domains (4)
         Sec.struct. author ..ee....eeeeee......eeeeee....eee.hhhhhhhhhhh..--------------.eee...ee..ee....eeeee.------------------------------------------..hhhhhhhhhhhhhhhhhh...eeeeeeeee..ee......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeee............hhhhhhhhhhhh.....eeee...hhhhh.hhhhhhh...---------........ee..ee....eeeeeee...-----------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------CHORISMATE_SYNTHA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA----------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-370 (gaps) UniProt: 1-376 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                          Transcript 1
                 1r52 D   1 MSTFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRR--------------RVEIQSGTEFGKTLGTPIAMMIK------------------------------------------RETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITREKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAMLAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFY---------TKTNNSGGVQGGISNGENIYFSVPFKSV-----------------------RHDPAVTPRAIPIVEAMTALVLADALLIQKARDF 370
                                    10        20        30        40      |  -         - |      70        80   |     -         -         -         -      |130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     |   -     | 290       300       310  |      -         -      |340       350       360       370
                                                                         47             62                    84                                        127                                                                                                                                                  276       286                        313                     337
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R52)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Chorismate_synt] (9)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AROC_YEAST | P28777)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0004107    chorismate synthase activity    Catalysis of the reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0042602    riboflavin reductase (NADPH) activity    Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  Cis Peptide Bonds
    Asp A:339 - Pro A:340   [ RasMol ]  
    Asp B:339 - Pro B:340   [ RasMol ]  
    Asp C:339 - Pro C:340   [ RasMol ]  
    Asp D:339 - Pro D:340   [ RasMol ]  
 

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  1r52
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  AROC_YEAST | P28777
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROC_YEAST | P28777: 1r53

(-) Related Entries Specified in the PDB File

1r53 THE SAME PROTEIN IN OTHER SPACE GROUP(I 2 2 2)