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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD+
 
Authors :  C. E. Nichols, J. Ren, K. Leslie, B. Dhaliwal, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Date :  25 Aug 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Shikimate Pathway, Aromatic Amino Acid Biosynthesis, Dhqs, Sadhqs, Open Form, Form B, Domain Movement, Cyclase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Nichols, J. Ren, K. Leslie, B. Dhaliwal, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Comparison Of Ligand Induced Conformational Changes And Domain Closure Mechanisms, Between Prokaryotic And Eukaryotic Dehydroquinate Synthases.
J. Mol. Biol. V. 343 533 2004
PubMed-ID: 15465043  |  Reference-DOI: 10.1016/J.JMB.2004.08.039
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMUT27
    Expression System Strain: BL21(DE3 PLYSS)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AROB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: SADHQS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:130 , GLU A:178 , HIS A:242 , HIS A:256 , NAD A:400BINDING SITE FOR RESIDUE ZN A 600
2AC2SOFTWAREASP B:130 , GLU B:178 , HIS B:242 , HIS B:256 , NAD B:401BINDING SITE FOR RESIDUE ZN B 601
3AC3SOFTWAREASP A:39 , TYR A:41 , VAL A:42 , TYR A:45 , PHE A:46 , GLY A:67 , GLU A:68 , LYS A:71 , GLY A:99 , GLY A:100 , ALA A:101 , ASP A:104 , THR A:124 , THR A:125 , LEU A:127 , ASP A:130 , SER A:131 , LYS A:136 , LYS A:145 , ASN A:146 , PHE A:163 , THR A:166 , LEU A:167 , GLN A:171 , LYS A:221 , HIS A:256 , ZN A:600 , HOH A:609 , HOH A:615 , HOH A:616 , HOH A:670 , GLN B:286BINDING SITE FOR RESIDUE NAD A 400
4AC4SOFTWAREGLN A:286 , ASP B:39 , TYR B:41 , VAL B:42 , TYR B:45 , PHE B:46 , GLY B:67 , GLU B:68 , LYS B:71 , GLY B:99 , GLY B:100 , ALA B:101 , ASP B:104 , THR B:124 , THR B:125 , LEU B:127 , ASP B:130 , SER B:131 , LYS B:136 , LYS B:145 , ASN B:146 , PHE B:163 , THR B:166 , LEU B:167 , GLN B:171 , LYS B:221 , ZN B:601 , HOH B:611 , HOH B:633BINDING SITE FOR RESIDUE NAD B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XAH)

(-) 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:323
 aligned with AROB_STAAR | Q6GGU4 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:352
                                    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       350  
           AROB_STAAR     1 MKLQTTYPSNNYPIFVEHGAIDHISTYIDQFDQSFILIDEHVNQYFADKFNDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFEQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLKGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDINHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLIRQFGDIVVQHVDQLTLQHACEQLKTY 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xahA01 A:1-166  [code=3.40.50.1970, no name define      d]                                                                                                           ----------------------------------------------------------------------------------------------------------------------------------                       --------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeee.hhhhhhhhhhh....eeeeeehhhhhhhhhhhh------.eeeeee.hhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhh.eeeeee...hhhhhh...eeee........eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....-----------------------....eeeee..eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xah A   1 MKLQTTYPSNNYPIYVEHGAIKYIGTYLNQFDQSFLLIDEYVNQYFANKFD------NVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFKQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLNGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDISHYIQYLIQLGYPLD-----------------------GVQMVLMRQFGDIVVQHVDQLTLQHACEQLKTY 352
                                    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     |   -         -       320       330       340       350  
                                                                             51     58                                                                                                                                                                                                                                           296                     320                                


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with AROB_STAAR | Q6GGU4 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:352
                                    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       350  
           AROB_STAAR     1 MKLQTTYPSNNYPIFVEHGAIDHISTYIDQFDQSFILIDEHVNQYFADKFNDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFEQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLKGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDINHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLIRQFGDIVVQHVDQLTLQHACEQLKTY 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xahB01 B:1-166  [code=3.40.50.1970, no name define      d]                                                                                                           ----------------------------------------------------------------------------------------------------------------------------------        -------        --------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------      ---DHQ_synthase-1xahB01 B:61-311                                                                                                                                                                                                                                      --------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------      ---DHQ_synthase-1xahB02 B:61-311                                                                                                                                                                                                                                      --------------------------------- Pfam domains (2)
         Sec.struct. author .eee........eeeee.hhhhhhhhhhh....eeeeeehhhhhhhhhhhh------.eeeeee.hhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhh.eeeeee...hhhhhh...eeee........eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....--------hhhhh..--------....eeeee..eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xah B   1 MKLQTTYPSNNYPIYVEHGAIKYIGTYLNQFDQSFLLIDEYVNQYFANKFD------NVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFKQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLNGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDISHYIQYLIQLGYPLD--------TLYQYML--------GVQMVLMRQFGDIVVQHVDQLTLQHACEQLKTY 352
                                    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       350  
                                                                             51     58                                                                                                                                                                                                                                           296      305   311      320
   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 1XAH)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AROB_STAAR | Q6GGU4)
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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  1xah
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
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  AROB_STAAR | Q6GGU4
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  4.2.3.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROB_STAAR | Q6GGU4: 1xag 1xai 1xaj 1xal

(-) Related Entries Specified in the PDB File

1nr5 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH COFACTOR AND SUBSTRATE ANALOGUE
1nrx CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD+, CRYSTAL FORM F, OPEN FORM WITH COFACTOR
1nua CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, APO, CRYSTAL FORM D, OPEN FORM
1nva CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND ADP, CRYSTAL FORM D, OPEN FORM WITH CO-FACTOR ANALOGUE
1nvb CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH SUBSTRATE ANALOGUE
1nvd CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM B, CLOSED FORM WITH SUBSTRATE ANALOGUE
1nve CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD+, CRYSTAL FORM E, OPEN FORM WITH CO-FACTOR
1nvf CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, ADP AND CBP, CRYSTAL FORM H, CLOSED FORM WITH CO-FACTOR ANALOGUE AND SUBSTRATE ANALOGUE
1xag CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CAR
1xai CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE
1xaj CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE
1xal CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE (SOAK)