Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE
 
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 :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Shikimate Pathway, Aromatic Amino Acid Biosynthesis, Dhqs, Sadhqs, Closed Form, Form A, 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
    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

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2CRB1Ligand/Ion[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:178 , HIS A:242 , HIS A:256 , NAD A:400 , CRB A:500BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWARETYR A:7 , PRO A:8 , ARG A:153BINDING SITE FOR RESIDUE CL A 602
3AC3SOFTWAREHOH A:717BINDING SITE FOR RESIDUE CL A 603
4AC4SOFTWAREHIS A:87 , ASP A:317 , HOH A:660BINDING SITE FOR RESIDUE CL A 606
5AC5SOFTWAREASP A:39 , TYR A:41 , VAL A:42 , TYR A:45 , 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 , CRB A:500 , ZN A:601 , HOH A:619 , HOH A:620 , HOH A:667 , HOH A:700BINDING SITE FOR RESIDUE NAD A 400
6AC6SOFTWAREARG A:115 , ASP A:130 , LYS A:136 , ASN A:146 , GLU A:178 , LYS A:181 , LYS A:221 , ARG A:235 , LEU A:238 , ASN A:239 , HIS A:242 , HIS A:246 , HIS A:256 , LYS A:314 , NAD A:400 , ZN A:601 , HOH A:620BINDING SITE FOR RESIDUE CRB A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XAG)

(-) 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:353
 aligned with AROB_STAAR | Q6GGU4 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:353
                                    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 MKLQTTYPSNNYPIFVEHGAIDHISTYIDQFDQSFILIDEHVNQYFADKFNDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFEQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLKGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDINHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLIRQFGDIVVQHVDQLTLQHACEQLKTYF 353
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xagA01 A:1-166  [code=3.40.50.1970, no name defined]                                                                                                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------DHQ_synthase-1xagA01 A:61-317                                                                                                                                                                                                                                    ------------------------------------ Pfam domains
         Sec.struct. author .eee........eeeee.hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhh.eeeeee...hhhhhh...eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..........eeeeeee..eeeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xag A   1 MKLQTTYPSNNYPIYVEHGAIKYIGTYLNQFDQSFLLIDEYVNQYFANKFDDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFKQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLNGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDISHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLMRQFGDIVVQHVDQLTLQHACEQLKTYF 353
                                    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
   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 1XAG)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CRB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xag)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1xag
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AROB_STAAR | Q6GGU4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.3.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AROB_STAAR | Q6GGU4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AROB_STAAR | Q6GGU4: 1xah 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
1xah CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD+
1xai CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ 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)