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(-) Description

Title :  CRYSTAL STRUCTURE OF PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM ESCHERICHIA COLI COMPLEXED WITH PB2+ AND PEP
 
Authors :  I. A. Shumilin, R. H. Kretsinger, R. H. Bauerle
Date :  18 Jun 99  (Deposition) - 31 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Alpha-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Shumilin, R. H. Kretsinger, R. H. Bauerle
Crystal Structure Of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Escherichia Coli.
Structure Fold. Des. V. 7 865 1999
PubMed-ID: 10425687  |  Reference-DOI: 10.1016/S0969-2126(99)80109-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO- HEPTULOSONATE-7-PHOSPHATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.1.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTA1
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE, DAHP SYNTHETASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1PB4Ligand/IonLEAD (II) ION
2PEP4Ligand/IonPHOSPHOENOLPYRUVATE
3SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:61 , HIS A:268 , GLU A:302 , ASP A:326 , PEP A:1352BINDING SITE FOR RESIDUE PB A 351
02AC2SOFTWARECYS B:61 , HIS B:268 , GLU B:302 , ASP B:326 , PEP B:2352BINDING SITE FOR RESIDUE PB B 351
03AC3SOFTWARECYS C:61 , HIS C:268 , GLU C:302 , ASP C:326 , PEP C:3352BINDING SITE FOR RESIDUE PB C 351
04AC4SOFTWARECYS D:61 , HIS D:268 , GLU D:302 , ASP D:326 , PEP D:4352BINDING SITE FOR RESIDUE PB D 351
05AC5SOFTWAREARG A:99 , THR A:100BINDING SITE FOR RESIDUE SO4 A 1353
06AC6SOFTWAREARG B:99 , THR B:100BINDING SITE FOR RESIDUE SO4 B 2353
07AC7SOFTWAREARG C:99 , THR C:100BINDING SITE FOR RESIDUE SO4 C 3353
08AC8SOFTWAREARG D:99 , THR D:100BINDING SITE FOR RESIDUE SO4 D 4353
09AC9SOFTWAREARG A:92 , TYR A:94 , LYS A:97 , GLY A:163 , ALA A:164 , ARG A:165 , LYS A:186 , ARG A:234 , HIS A:268 , PB A:351BINDING SITE FOR RESIDUE PEP A 1352
10BC1SOFTWAREARG B:92 , TYR B:94 , LYS B:97 , GLY B:163 , ALA B:164 , ARG B:165 , LYS B:186 , ARG B:234 , HIS B:268 , PB B:351BINDING SITE FOR RESIDUE PEP B 2352
11BC2SOFTWAREARG C:92 , TYR C:94 , LYS C:97 , GLY C:163 , ALA C:164 , ARG C:165 , LYS C:186 , ARG C:234 , HIS C:268 , PB C:351BINDING SITE FOR RESIDUE PEP C 3352
12BC3SOFTWAREARG D:92 , TYR D:94 , LYS D:97 , GLY D:163 , ALA D:164 , ARG D:165 , LYS D:186 , ARG D:234 , HIS D:268 , PB D:351BINDING SITE FOR RESIDUE PEP D 4352

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QR7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QR7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QR7)

(-) Exons   (0, 0)

(no "Exon" information available for 1QR7)

(-) 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:338
 aligned with AROG_ECOLI | P0AB91 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:343
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347   
           AROG_ECOLI     8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
               SCOP domains d1qr7a_ A: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG)                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1qr7A00 A:8-350 Aldolase class I                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeeehhhhh.hhhhhhhhh.....eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhhhhhh....eeeeeee..........-----............hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qr7 A   8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSL-----LAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    |    -|      327       337       347   
                                                                                                                                                                                                                                                                                                                                          312   318                                


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with AROG_ECOLI | P0AB91 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:343
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347   
           AROG_ECOLI     8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
               SCOP domains d1qr7b_ B: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG)                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1qr7B00 B:8-350 Aldolase class I                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeeehhhhh.hhhhhhhhh.....eeee......hhhhhhhhhhhh...eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhhhhhh....eeeeeee..........-----............hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qr7 B   8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSL-----LAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    |    -|      327       337       347   
                                                                                                                                                                                                                                                                                                                                          312   318                                


Chain C from PDB  Type:PROTEIN  Length:338
 aligned with AROG_ECOLI | P0AB91 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:343
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347   
           AROG_ECOLI     8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
               SCOP domains d1qr7c_ C: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG)                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1qr7C00 C:8-350 Aldolase class I                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhh.eeeehhhhh.hhhhhhhhhh....eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee.hhhhhh...hhhhhhhhhhhhhhhh....eeeeeee...eeee...-----....ee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qr7 C   8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSL-----LAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    |    -|      327       337       347   
                                                                                                                                                                                                                                                                                                                                          312   318                                


Chain D from PDB  Type:PROTEIN  Length:339
 aligned with AROG_ECOLI | P0AB91 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:343
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347   
           AROG_ECOLI     8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
               SCOP domains d1qr7d_ D: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG)                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1qr7D00 D:8-350 Aldolase class I                                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----------------DAHP_synth_1-1qr7D01 D:25-339                                                                                                                                                                                                                                                                                              ----------- Pfam domains (1)
           Pfam domains (2) -----------------DAHP_synth_1-1qr7D02 D:25-339                                                                                                                                                                                                                                                                                              ----------- Pfam domains (2)
           Pfam domains (3) -----------------DAHP_synth_1-1qr7D03 D:25-339                                                                                                                                                                                                                                                                                              ----------- Pfam domains (3)
           Pfam domains (4) -----------------DAHP_synth_1-1qr7D04 D:25-339                                                                                                                                                                                                                                                                                              ----------- Pfam domains (4)
         Sec.struct. author ..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.eeee......hhhhhhhhhh....eeee......hhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee........hhhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhhhh....eeeeeee..........----.............hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qr7 D   8 LRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSL----PLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    |  317       327       337       347   
                                                                                                                                                                                                                                                                                                                                          312  317
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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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AROG_ECOLI | P0AB91)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
cellular component
    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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  1qr7
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROG_ECOLI | P0AB91: 1gg1 1kfl 1n8f 5cks

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QR7)