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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (DAHP SYNTHASE) (TM0343) FROM THERMOTOGA MARITIMA AT 1.92 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 Feb 05  (Deposition) - 08 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tm0343, Phospho-2-Dehydro-3-Deoxyheptonate Aldolase (Ec 2. 5. 1. 54) (Dahp Synthase), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Phospho-2-Dehydro-3-Deoxyheptonate Aldolase (Dahp Synthase) (Tm0343) From Thermotoga Maritima At 1. 92 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 2.5.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0343
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE, DAHP SYNTHETASE, 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE

 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 1VR6)

(-) Sites  (0, 0)

(no "Site" information available for 1VR6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VR6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VR6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VR6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VR6)

(-) Exons   (0, 0)

(no "Exon" information available for 1VR6)

(-) 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 AROF_THEMA | Q9WYH8 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:343
                                 1                                                                                                                                                                                                                                                                                                                                                 
                                 |   5        15        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   
           AROF_THEMA     - -----MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
               SCOP domains d1vr6a_ A: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1vr6A01 A:-4-70 Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1      1vr6A02 A:71-338 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhh.eeeeeee....eeeeeeeee...hhhhhhh...eeeeee..................ee....ee...eeeeeee.....hhhhhhhhhhhhhhh...eee................hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh....eeeee................hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr6 A  -4 HHHHHMIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
                                     5        15        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   


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with AROF_THEMA | Q9WYH8 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:342
                                1                                                                                                                                                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336  
           AROF_THEMA     - ----MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
               SCOP domains d1vr6b_ B: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1vr6B01 B:-3-70 Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1     1vr6B02 B:71-338 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhh.eeeeeee....eeeeeeee....hhhhhhh...eeeeee..................ee....ee...eeeeeee.....hhhhhhhhhhhhhhh...eee.......----.....hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhh.eeee.hhhh.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.....eeeee................hhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeeee...hhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vr6 B  -3 HHHHMIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPR----SFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
                                     6        16        26        36        46        56        66        76        86        96       106       116       126      |  - |     146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336  
                                                                                                                                                                  133  138                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:339
 aligned with AROF_THEMA | Q9WYH8 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:343
                                 1                                                                                                                                                                                                                                                                                                                                                 
                                 |   5        15        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   
           AROF_THEMA     - -----MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
               SCOP domains d1vr6c_ C: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1vr6C01 C:-4-70 Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1      1vr6C02 C:71-338 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhh..eeeeee....eeeeeeee....hhhhhhh...eeeeee..................ee....ee...eeeeeee.....hhhhhhhhhhhhhhh...eee........----....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhh.....eeeee................hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr6 C  -4 HHHHHMIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRT----FQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
                                     5        15        25        35        45        55        65        75        85        95       105       115       125        |-   |   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335   
                                                                                                                                                                    134  139                                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:340
 aligned with AROF_THEMA | Q9WYH8 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:341
                               1                                                                                                                                                                                                                                                                                                                                                 
                               |     7        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 
           AROF_THEMA     - ---MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
               SCOP domains d1vr6d_ D: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vr6D01 D:-2-70 Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1    1vr6D02 D:71-338 Aldolase class I                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) -----------------------------------------------------------------------DAHP_synth_1-1vr6D01 D:69-333                                                                                                                                                                                                                                            ----- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------DAHP_synth_1-1vr6D02 D:69-333                                                                                                                                                                                                                                            ----- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------DAHP_synth_1-1vr6D03 D:69-333                                                                                                                                                                                                                                            ----- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------DAHP_synth_1-1vr6D04 D:69-333                                                                                                                                                                                                                                            ----- Pfam domains (4)
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhh..eeeeee....eeeeeee.....hhhhhhh...eeeeee..................ee....ee...eeeeeee.....hhhhhhhhhhhhhhh...eee..........-.....hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhh.eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh....eeeee................hhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeeee...hhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr6 D  -2 HHHMIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSP-SFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN 338
                                     7        17        27        37        47        57        67        77        87        97       107       117       127        |-|      147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
                                                                                                                                                                    136 |                                                                                                                                                                                                        
                                                                                                                                                                      138
   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  (1, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AROF_THEMA | Q9WYH8)
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:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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

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UniProtKB/Swiss-Prot
        AROF_THEMA | Q9WYH8: 1rzm 3pg8 3pg9 4grs

(-) Related Entries Specified in the PDB File

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