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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH PHOSPHOENOLPYRUVATE AND COBALT(II)
 
Authors :  V. Koenig, A. Pfeil, G. Heinrich, G. H. Braus, T. R. Schneider
Date :  09 Apr 03  (Deposition) - 08 Apr 04  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Barrel, Lyase, Aromatic Amino-Acid Biosynthesis Synthase, Aldolase, Synthetase, Manganese (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Koenig, A. Pfeil, G. H. Braus, T. R. Schneider
Substrate And Metal Complexes Of 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Provide New Insights Into The Catalytic Mechanism
J. Mol. Biol. V. 337 675 2004
PubMed-ID: 15019786  |  Reference-DOI: 10.1016/J.JMB.2004.01.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.15
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Taxid: 4932
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: LIGAND: PHOSPHOENOLPYRUVATE METAL: COBALT(II)
    Strain: RH1326
    Synonym: PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE DAHP SYNTHETASE, 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE, PHOSPHO-2-DEHYDRO- 3-DEOXYHEPTONATE ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2GOL3Ligand/IonGLYCEROL
3PEP2Ligand/IonPHOSPHOENOLPYRUVATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2143 , CYS B:76 , HIS B:282 , GLU B:316 , ASP B:342BINDING SITE FOR RESIDUE CO A 400
2AC2SOFTWARECYS A:76 , HIS A:282 , GLU A:316 , ASP A:342 , PEP A:508 , HOH B:2141BINDING SITE FOR RESIDUE CO B 400
3AC3SOFTWAREARG A:107 , TYR A:109 , LYS A:112 , GLY A:178 , ALA A:179 , ARG A:180 , LYS A:201 , ARG A:249 , HIS A:282 , HOH A:2057 , HOH A:2069 , HOH A:2144 , HOH A:2145 , CO B:400 , HOH B:2141BINDING SITE FOR RESIDUE PEP A 508
4AC4SOFTWAREHOH A:2143 , ARG B:107 , TYR B:109 , LYS B:112 , GLY B:178 , ALA B:179 , ARG B:180 , LYS B:201 , ARG B:249 , HIS B:282 , HOH B:2035 , HOH B:2142 , HOH B:2143BINDING SITE FOR RESIDUE PEP B 508
5AC5SOFTWAREGLU A:111 , ASP A:161 , HOH A:2031 , HOH A:2060 , HOH A:2061 , GLN B:185 , LEU B:186 , GLU B:189 , PHE B:224BINDING SITE FOR RESIDUE GOL A 601
6AC6SOFTWAREGLN A:185 , GLU A:189 , PHE A:224 , GLU B:111 , ASP B:161 , HOH B:2066 , HOH B:2144BINDING SITE FOR RESIDUE GOL B 601
7AC7SOFTWAREHOH A:2143 , LYS B:112 , PRO B:113 , THR B:341 , ASP B:342 , HOH B:2142BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OFA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OFA)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR249C1YBR249C.1II:717989-7168771113AROG_YEAST1-3703702A:23-369 (gaps)
B:23-369 (gaps)		347
347

(-) 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:343
 aligned with AROG_YEAST | P32449 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:347
                                    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       352       362       
           AROG_YEAST    23 VRILGYDPLASPALLQVQIPATPTSLETAKRGRREAIDIITGKDDRVLVIVGPCSIHDLEAAQEYALRLKKLSDELKGDLSIIMRAYLEKPRTTVGWKGLINDPDVNNTFNINKGLQSARQLFVNLTNIGLPIGSEMLDTISPQYLADLVSFGAIGARTTESQLHRELASGLSFPVGFKNGTDGTLNVAVDACQAAAHSHHFMGVTKHGVAAITTTKGNEHCFVILRGGKKGTNYDAKSVAEAKAQLPAGSNGLMIDYSHGNSNKDFRNQPKVNDVVCEQIANGENAITGVMIESNINEGNQGIPAEGKAGLKYGVSITDACIGWETTEDVLRKLAAAVRQRREVNK 369
               SCOP domains d1ofaa_ A: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG)                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1ofaA00 A:23-369 Aldolase class I                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeeeee.......hhhhhhhhhhhh......eeeeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee...........----..............hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:23-369 (gaps) UniProt: 1-370 [INCOMPLETE]                                                                                                                                                                                                                                                                                                  Transcript 1
                 1ofa A  23 VRILGYDPLASPALLQVQIPATPTSLETAKRGRREAIDIITGKDDRVLVIVGPCSIHDLEAAQEYALRLKKLSDELKGDLSIIMRAYLEKPRTTVGWKGLINDPDVNNTFNINKGLQSARQLFVNLTNIGLPIGSEMLDTISPQYLADLVSFGAIGARTTESQLHRELASGLSFPVGFKNGTDGTLNVAVDACQAAAHSHHFMGVTKHGVAAITTTKGNEHCFVILRGGKKGTNYDAKSVAEAKAQLPAGSNGLMIDYSHGNSNKDFRNQPKVNDVVCEQIANGENAITGVMIESNINEGNQGIP----AGLKYGVSITDACIGWETTEDVLRKLAAAVRQRREVNK 369
                                    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       352       362       
                                                                                                                                                                                                                                                                                                                                          327  332                                     


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with AROG_YEAST | P32449 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:347
                                    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       352       362       
           AROG_YEAST    23 VRILGYDPLASPALLQVQIPATPTSLETAKRGRREAIDIITGKDDRVLVIVGPCSIHDLEAAQEYALRLKKLSDELKGDLSIIMRAYLEKPRTTVGWKGLINDPDVNNTFNINKGLQSARQLFVNLTNIGLPIGSEMLDTISPQYLADLVSFGAIGARTTESQLHRELASGLSFPVGFKNGTDGTLNVAVDACQAAAHSHHFMGVTKHGVAAITTTKGNEHCFVILRGGKKGTNYDAKSVAEAKAQLPAGSNGLMIDYSHGNSNKDFRNQPKVNDVVCEQIANGENAITGVMIESNINEGNQGIPAEGKAGLKYGVSITDACIGWETTEDVLRKLAAAVRQRREVNK 369
               SCOP domains d1ofab_ B: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG)                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1ofaB00 B:23-369 Aldolase class I                                                                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) -----------------DAHP_synth_1-1ofaB01 B:40-355                                                                                                                                                                                                                                                                                               -------------- Pfam domains (1)
           Pfam domains (2) -----------------DAHP_synth_1-1ofaB02 B:40-355                                                                                                                                                                                                                                                                                               -------------- Pfam domains (2)
         Sec.struct. author ..eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee.........hhhhhhhhhhhh......eeee.hhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee.........---------...........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:23-369 (gaps) UniProt: 1-370 [INCOMPLETE]                                                                                                                                                                                                                                                                                                  Transcript 1
                 1ofa B  23 VRILGYDPLASPALLQVQIPATPTSLETAKRGRREAIDIITGKDDRVLVIVGPCSIHDLEAAQEYALRLKKLSDELKGDLSIIMRAYLEKPRTTVGWKGLINDPDVNNTFNINKGLQSARQLFVNLTNIGLPIGSEMLDTISPQYLADLVSFGAIGARTTESQLHRELASGLSFPVGFKNGTDGTLNVAVDACQAAAHSHHFMGVTKHGVAAITTTKGNEHCFVILRGGKKGTNYDAKSVAEAKAQLPAGSNGLMIDYSHGNSNKDFRNQPKVNDVVCEQIANGENAITGVMIESNINEGNQG---------KYGVSITDACIGWETTEDVLRKLAAAVRQRREVNK 369
                                    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  |      -  |    342       352       362       
                                                                                                                                                                                                                                                                                                                                        325       335
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AROG_YEAST | P32449)
molecular function
    GO:0003849    3-deoxy-7-phosphoheptulonate synthase activity    Catalysis of the reaction: D-erythrose 4-phosphate + H(2)O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AROG_YEAST | P32449: 1hfb 1oab 1of6 1of8 1ofb 1ofo 1ofp 1ofq 1ofr 1og0

(-) Related Entries Specified in the PDB File

1hfb CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHOSPHOENOLPYRUVATE
1oab CRYSTAL STRUCTURE OF 3-DEOXY-D-ARABINO- HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH PHOSPHOENOLPYRUVATE AND MANGANESE(II)
1of6 CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH TYROSINE AND MANGANESE
1of8 DOUBLE COMPLEX OF THE TYROSINE SENSITIVE DAHP SYNTHASE FROM S. CEREVISIAE WITH CO2 +, PEP AND THE E4P ANALOGOUE G3P
1ofb CRYSTAL STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH MANGANESE(II)