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Title :   2.4A CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS TYPE I 3-DEHYDROQUINASE, WITH 3-DEHYDROQUINATE BOUND

Authors :   C. E. Nichols, M. Lockyer, A. R. Hawkins, D. K. Stammers

Date :   19 Feb 04 (Deposition) - 12 Oct 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   3-Dehydroquinase, Enzyme Turnover, Shikimate Pathway, 3- Dehydroquinate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Nichols, M. Lockyer, A. R. Hawkins, D. K. Stammers
Crystal Structures Of Staphylococcus Aureus Type I Dehydroquinase From Enzyme Turnover Experiments
Proteins V. 56 625 2004
PubMed-ID: 15229896 | Reference-DOI: 10.1002/PROT.20165

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PRF88
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PRSETB
	Gene	:	AROD
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	282458
	Strain	:	MRSA252
	Synonym	:	3-DEHYDROQUINASE, TYPE I DHQASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	DHK	2	Ligand/Ion	3-DEHYDROSHIKIMATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:9 , GLU A:35 , ARG A:37 , ARG A:70 , HIS A:133 , LYS A:160 , ARG A:202 , TYR A:214 , ALA A:222 , GLN A:225	BINDING SITE FOR RESIDUE DHK A 239
2	AC2	SOFTWARE	THR B:9 , GLU B:35 , ARG B:37 , ARG B:70 , HIS B:133 , LYS B:160 , ARG B:202 , TYR B:214 , ALA B:222 , GLN B:225 , HOH B:342	BINDING SITE FOR RESIDUE DHK B 239

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

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

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

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

(no "Exon" information available for 1SFJ)

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:227
 aligned with AROD_STAAR | Q6GII7 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      
           AROD_STAAR     3 HVEVVATITPQLYIEETLIQKINHRIDAIDVLELRIDQFENVTVDQVAEMITKLKVMQDSFKLLVTYRTKLQGGYGQFTNDSYLNLISDLANINGIDMIDIEWQADIDIEKHQRIITHLQQYNKEVIISHHNFESTPPLDELQFIFFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKVVGISMSKLGLISRTAQGVFGGALTYGCIGEPQAPGQIDVTDLKAQVTLY 238
               SCOP domains d1sfja_ A:     Type I 3-dehydroquinate dehydratase                                                                                                                                                                                           SCOP domains
               CATH domains 1sfjA00 A:3    -238 Aldolase class I                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...----hhhhhhhhhh.....eeeee.......hhhhhhhhhh..-----..eeeee..hhhhh.....hhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.......eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sfj A   3 HVEVVATITPQ----ETLIQKINHRIDAIDVLELRIDQFENVTVDQVAEMITKL-----SFKLLVTYRTKLQGGYGQFTNDSYLNLISDLANINGIDMIDIEWQADIDIEKHQRIITHLQQYNKEVIISHHNFESTPPLDELQFIFFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKVVGISMSKLGLISRTAQGVFGGALTYGCIGEPQAPGQIDVTDLKAQVTLY 238
                                    12|    |  22        32        42        52   |    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      
                                     13   18                                    56    62

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with AROD_STAAR | Q6GII7 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           AROD_STAAR     1 MTHVEVVATITPQLYIEETLIQKINHRIDAIDVLELRIDQFENVTVDQVAEMITKLKVMQDSFKLLVTYRTKLQGGYGQFTNDSYLNLISDLANINGIDMIDIEWQADIDIEKHQRIITHLQQYNKEVIISHHNFESTPPLDELQFIFFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKVVGISMSKLGLISRTAQGVFGGALTYGCIGEPQAPGQIDVTDLKAQVTLY 238
               SCOP domains d1sfjb_ B: Type   I 3-dehydroquinate dehydratase                                                                                                                                                                                               SCOP domains
               CATH domains 1sfjB00 B:1-238   Aldolase class I                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....--hhhhhhhhhh.....eeeee.......hhhhhhhhhhh.---....eeeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.......eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sfj B   1 MTHVEVVATITPQLY--ETLIQKINHRIDAIDVLELRIDQFENVTVDQVAEMITKL---QDSFKLLVTYRTKLQGGYGQFTNDSYLNLISDLANINGIDMIDIEWQADIDIEKHQRIITHLQQYNKEVIISHHNFESTPPLDELQFIFFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDCKVVGISMSKLGLISRTAQGVFGGALTYGCIGEPQAPGQIDVTDLKAQVTLY 238
                                    10    |  |20        30        40        50     |  60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
                                         15 18                                    56  60

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: Class I aldolase (182)

Protein domain: Type I 3-dehydroquinate dehydratase (6)

Staphylococcus aureus [TaxId: 1280] (2)

1a	d1sfja_	A:
1b	d1sfjb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Aureus mrsa252 (Staphylococcus aureus subsp) (2)

1a	1sfjB00	B:1-238
1b	1sfjA00	A:3-238

(no "Pfam Domain" information available for 1SFJ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AROD_STAAR | Q6GII7)

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.

Asymmetric/Biological Unit
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	AROD_STAAR \| Q6GII7	:	1sfl

1sfl	1.9A CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS TYPE I 3- DEHYDROQUINASE, APO FORM

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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