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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE FROM AQUIFEX AEOLICUS VF5
 
Authors :  T. Tanaka, T. S. Kumarevel, A. Ebihara, L. Chen, Z. Q. Fu, J. Chrzas, B. C. S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Apr 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  3-Dehydroquinate Dehydratase, Aquifex Aeolicus Vf5, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. S. Kumarevel, T. Tanaka, S. Kuramitsu, S. Yokoyama
Crystal Structure Of The 3-Dehydroquinate Dehydratase From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    ChainsA, B, C
    EC Number4.2.1.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System StrainBL21(DE3)CODONPLUS-RIL-X
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid224324
    StrainVF5
    Synonym3-DEHYDROQUINASE, TYPE I DHQASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)AB 
Biological Unit 2 (2x)  C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2YSW)

(-) Sites  (0, 0)

(no "Site" information available for 2YSW)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:158 -B:158
2C:158 -C:158

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YSW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IPS01028 Dehydroquinase class I active site.AROD_AQUAE88-117
 
 
  3A:88-117
B:88-117
C:88-117
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IPS01028 Dehydroquinase class I active site.AROD_AQUAE88-117
 
 
  2A:88-117
B:88-117
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IPS01028 Dehydroquinase class I active site.AROD_AQUAE88-117
 
 
  2-
-
C:88-117

(-) Exons   (0, 0)

(no "Exon" information available for 2YSW)

(-) Sequences/Alignments

Asymmetric 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:219
 aligned with AROD_AQUAE | O66440 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           AROD_AQUAE     1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
               SCOP domains d2yswa_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh...eeeee.hhh...hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh......eeeee.....hhhhhhhhhh..eee............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:88-11------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysw A   1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with AROD_AQUAE | O66440 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           AROD_AQUAE     1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
               SCOP domains d2yswb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh...eeeee.hhh...hhhhhhhhhhhhhhh..eeeee..hhhhh.....hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh..eee............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:88-11------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysw B   1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with AROD_AQUAE | O66440 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           AROD_AQUAE     1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
               SCOP domains d2yswc_ C: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DHquinase_I-2yswC01 C:3-214                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) --DHquinase_I-2yswC02 C:3-214                                                                                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) --DHquinase_I-2yswC03 C:3-214                                                                                                                                                                                         ----- Pfam domains (3)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh..eeeee..hhhhh.....hhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh......eeeee.....hhhhhhhhhh..eee............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: C:88-11------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysw C   1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (AROD_AQUAE | O66440)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    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.
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.

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 Related Entries

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        AROD_AQUAE | O664402egz

(-) Related Entries Specified in the PDB File

2egz DIFFERENT SPACE GROUP RELATED ID: AAE001000021.2 RELATED DB: TARGETDB