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(-) Description

Title :  CRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Sugahara, S. Yokoyama, S. Kuramitsu, M. Miyano, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Aug 03  (Deposition) - 02 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydroquinate Synthase, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, Y. Nodake, M. Sugahara, N. Kunishima
Crystal Structure Of Dehydroquinate Synthase From Thermus Thermophilus Hb8 Showing Functional Importance Of The Dimeric State.
Proteins V. 58 249 2005
PubMed-ID: 15508124  |  Reference-DOI: 10.1002/PROT.20281

(-) Compounds

Molecule 1 - DEHYDROQUINATE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1UJN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:8 -Pro A:9
2Glu B:8 -Pro B:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UJN)

(-) 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 P83703_THETH | P83703 from UniProtKB/TrEMBL  Length:348

    Alignment length:347
                                    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       
         P83703_THETH     1 MQRLEVREPVPYPILVGEGVLKEVPPLAGPAALLFDRRVEGFAQEVAKALGVRHLLGLPGGEAAKSLEVYGKVLSWLAEKGLPRNATLLVVGGGTLTDLGGFVAATYLRGVAYLAFPTTTLAIVDASVGGKTGINLPEGKNLVGAFHFPQGVYAELRALKTLPLPTFKEGLVEAFKHGLIAGDEALLKVEDLTPQSPRLEAFLARAVAVKVRVTEEDPLEKGKRRLLNLGHTLGHALEAQTRHALPHGMAVAYGLLYAALLGRALGGEDLLPPVRRLLLWLSPPPLPPLAFEDLLPYLLRDKKKVSESLHWVVPLAPGRLVVRPLPEGLLREAFAAWREELKGLGLL 347
               SCOP domains d1ujna_ A: Dehydroquinate synthase, DHQS                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1ujnA01 A:1-161  [code=3.40.50.1970, no name defined]                                                                                                            1ujnA02 A:162-338 Dehydroquinate synthase-like - alpha domain                                                                                                                    --------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeee.hhhhhh......eeeeee..hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhh---------...eeeeee..eeeee..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ujn A   1 MQRLEVREPVPYPILVGEGVLKEVPPLAGPAALLFDRRVEGFAQEVAKALGVRHLLGLPGGEAAKSLEVYGKVLSWLAEKGLPRNATLLVVGGGTLTDLGGFVAATYLRGVAYLAFPTTTLAIVDASVGGKTGINLPEGKNLVGAFHFPQGVYAELRALKTLPLPTFKEGLVEAFKHGLIAGDEALLKVEDLTPQSPRLEAFLARAVAVKVRVTEEDPLEKGKRRLLNLGHTLGHALEAQTRHALPHGMAVAYGLLYAALLGRALGGEDLLPPVRRLLLWLSPPPLPPLAFEDLLPYL---------SLHWVVPLAPGRLVVRPLPEGLLREAFAAWREELKGLGLL 347
                                    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       | -       310       320       330       340       
                                                                                                                                                                                                                                                                                                                                   298       308                                       


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with P83703_THETH | P83703 from UniProtKB/TrEMBL  Length:348

    Alignment length:348
                                    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        
         P83703_THETH     1 MQRLEVREPVPYPILVGEGVLKEVPPLAGPAALLFDRRVEGFAQEVAKALGVRHLLGLPGGEAAKSLEVYGKVLSWLAEKGLPRNATLLVVGGGTLTDLGGFVAATYLRGVAYLAFPTTTLAIVDASVGGKTGINLPEGKNLVGAFHFPQGVYAELRALKTLPLPTFKEGLVEAFKHGLIAGDEALLKVEDLTPQSPRLEAFLARAVAVKVRVTEEDPLEKGKRRLLNLGHTLGHALEAQTRHALPHGMAVAYGLLYAALLGRALGGEDLLPPVRRLLLWLSPPPLPPLAFEDLLPYLLRDKKKVSESLHWVVPLAPGRLVVRPLPEGLLREAFAAWREELKGLGLLR 348
               SCOP domains d1ujnb_ B: Dehydroquinate synthase, DHQS                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ujnB01 B:1-161  [code=3.40.50.1970, no name defined]                                                                                                            1ujnB02 B:162-338 Dehydroquinate synthase-like - alpha domain                                                                                                                    ---------- CATH domains
           Pfam domains (1) ------------------------------------------------------DHQ_synthase-1ujnB01 B:55-298                                                                                                                                                                                                                                ----------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------DHQ_synthase-1ujnB02 B:55-298                                                                                                                                                                                                                                ----------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee.....eeeeee.hhhhhh......eeeeee..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh....eeeeee..eeeeeeee....eeeee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.---..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhh---------..eeeeeee..eeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ujn B   1 MQRLEVREPVPYPILVGEGVLKEVPPLAGPAALLFDRRVEGFAQEVAKALGVRHLLGLPGGEAAKSLEVYGKVLSWLAEKGLPRNATLLVVGGGTLTDLGGFVAATYLRGVAYLAFPTTTLAIVDASVGGKTGINLPEGKNLVGAFHFPQGVYAELRALKTLPLPTFKEGLVEAFKHGLIAGDEALLKVEDLTPQSPRLEAFLARAVAVKVRVTEEDPLEKGKRRLLNLGHTLGHALEAQ---ALPHGMAVAYGLLYAALLGRALGGEDLLPPVRRLLLWLSPPPLPPLAFEDLLPYL---------SLHWVVPLAPGRLVVRPLPEGLLREAFAAWREELKGLGLLR 348
                                    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       | -       310       320       330       340        
                                                                                                                                                                                                                                                                         240 244                                                   298       308
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P83703_THETH | P83703)
molecular function
    GO:0003856    3-dehydroquinate synthase activity    Catalysis of the reaction: 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate.
    GO:0016838    carbon-oxygen lyase activity, acting on phosphates    Catalysis of the cleavage of a carbon-oxygen bond by elimination of a 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.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Glu A:8 - Pro A:9   [ RasMol ]  
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