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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS DEHYDROQUINATE DEHYDRATASE-SHIKIMATE DEHYDROGENASE IN COMPLEX WITH TARTRATE AND SHIKIMATE
 
Authors :  S. A. Singh, D. Christendat
Date :  18 Apr 06  (Deposition) - 06 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Type I Dehydroquinate Dehydratase, Aroe, Shikimate Dehydrogenase, Arabidopsis Thaliana, Shikimate, Tartrate, Bifunctional Enzyme, Oxidoreductase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. A. Singh, D. Christendat
Structure Of Arabidopsis Dehydroquinate Dehydratase-Shikimate Dehydrogenase And Implications For Metabolic Channeling In The Shikimate Pathway
Biochemistry V. 45 7787 2006
PubMed-ID: 16784230  |  Reference-DOI: 10.1021/BI060366+
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE/ SHIKIMATE 5- DEHYDROGENASE
    ChainsA
    EC Number4.2.1.10, 1.1.1.25
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1SKM1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
2SO42Ligand/IonSULFATE ION
3TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:382 , PRO A:383 , HIS A:384 , LYS A:385 , GLU A:386 , GLY A:462 , GLY A:463 , HOH A:5062 , HOH A:5081 , HOH A:5125BINDING SITE FOR RESIDUE SO4 A 1402
2AC2SOFTWARETRP A:158 , PRO A:332 , PRO A:527 , HOH A:4996BINDING SITE FOR RESIDUE SO4 A 1403
3AC3SOFTWAREARG A:155 , HIS A:214 , LYS A:241 , MET A:271 , ARG A:279 , ALA A:301 , GLN A:304 , HOH A:5038 , HOH A:5066 , HOH A:5075 , HOH A:5210BINDING SITE FOR RESIDUE TLA A 4988
4AC4SOFTWAREILE A:328 , SER A:336 , SER A:338 , SER A:379 , THR A:381 , LYS A:385 , ASN A:406 , ASP A:423 , TYR A:550 , GLN A:578 , GLN A:582 , HOH A:5028BINDING SITE FOR RESIDUE SKM A 4733

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GPT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:331 -Pro A:332
2Ile A:382 -Pro A:383
3Gln A:526 -Pro A:527
4Thr A:551 -Pro A:552

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GPT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GPT)

(-) Exons   (0, 0)

(no "Exon" information available for 2GPT)

(-) 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:498
 aligned with DHQSD_ARATH | Q9SQT8 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:523
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           603         
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599   |     -   
          DHQSD_ARATH    90 VKNPSLICAPVMADSIDKMVIETSKAHELGADLVEIRLDWLKDFNPLEDLKTIIKKSPLPTLFTYRPKWEGGQYEGDENERRDVLRLAMELGADYIDVELQVASEFIKSIDGKKPGKFKVIVSSHNYQNTPSVEDLDGLVARIQQTGADIVKIATTAVDIADVARMFHITSKAQVPTIGLVMGERGLMSRILCSKFGGYLTFGTLDSSKVSAPGQPTIKDLLDLYNFRRIGPDTKVYGIIGKPVSHSKSPIVHNQAFKSVDFNGVYVHLLVDNLVSFLQAYSSSDFAGFSCTIPHKEAALQCCDEVDPLAKSIGAVNTILRRKSDGKLLGYNTDCIGSISAIEDGLRSSGDPSSVPSSSSPLASKTVVVIGAGGAGKALAYGAKEKGAKVVIANRTYERALELAEAIGGKALSLTDLDNYHPEDGMVLANTTSMGMQPNVEETPISKDALKHYALVFDAVYTPRITRLLREAEESGAITVSGSEMFVRQAYEQFEIFTGLPAPKELYWQIMSKY---------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...hhhhhhhhhhhhhhhh..eeeee.hhh...hhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh........eeeeeee......hhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhh.......eee..............hhhhhhhh.hhhhh....eeeeeee......hhhhhhhhhhhhh...eeeeeee..hhhhhhhhh....eeeeee...hhhhhhhhh.eehhhhhhhh...eeee......eeee.hhhhhhhhhhhhhh-------------------.eeee..hhhhhhhhhhhhhh...eeee......--hhhhhhh--..hhhhhh..--...eeeee..................hhh.eeeeee.......hhhhhhhhh...eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gpt A  90 VKNPSLICAPVMADSIDKMVIETSKAHELGADLVEIRLDWLKDFNPLEDLKTIIKKSPLPTLFTYRPKWEGGQYEGDENERRDVLRLAMELGADYIDVELQVASEFIKSIDGKKPGKFKVIVSSHNYQNTPSVEDLDGLVARIQQTGADIVKIATTAVDIADVARMFHITSKAQVPTIGLVMGERGLMSRILCSKFGGYLTFGTLDSSKVSAPGQPTIKDLLDLYNFRRIGPDTKVYGIIGKPVSHSKSPIVHNQAFKSVDFNGVYVHLLVDNLVSFLQAYSSSDFAGFSCTIPHKEAALQCCDEVDPLAKSIGAVNTILRRKSDGKLLGYNTDCIGSISAIEDGL-------------------TVVVIGAGGAGKALAYGAKEKGAKVVIANRTYER--ELAEAIG--ALSLTDLDNY--EDGMVLANTTSMGMQPNVEETPISKDALKHYALVFDAVYTPRITRLLREAEESGAITVSGSEMFVRQAYEQFEIFTGLPAPKELYWQIMSKYGSRENLYFQ 612
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429     |   -         -     | 459       469       479        |- |     | -|      509  |    519       529       539       549       559       569       579       589       599       609   
                                                                                                                                                                                                                                                                                                                                                                                   435                 455                              488  |   497  |      509  |                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                           491      500         512                                                                                                    

   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  (0, 0)

(no "SCOP Domain" information available for 2GPT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GPT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GPT)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DHQSD_ARATH | Q9SQT8)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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: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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + 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:0009793    embryo development ending in seed dormancy    The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
    GO:0019632    shikimate metabolic process    The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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        DHQSD_ARATH | Q9SQT82o7q 2o7s

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