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Title :   1.03 ANGSTROM CRYSTAL STRUCTURE OF Q236A MUTANT TYPE I DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM

Authors :   S. H. Light, G. Minasov, L. Shuvalova, L. Papazisi, W. F. Anderson, Cent Structural Genomics Of Infectious Diseases (Csgid)

Date :   21 Jul 10 (Deposition) - 11 Aug 10 (Release) - 04 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.03

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

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, Dehydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Light, G. Minasov, L. Shuvalova, S. N. Peterson, M. Caffrey, W. F. Anderson, A. Lavie
A Conserved Surface Loop In Type I Dehydroquinate Dehydratases Positions An Active Site Arginine And Function In Substrate Binding.
Biochemistry V. 50 2357 2011
PubMed-ID: 21291284 | Reference-DOI: 10.1021/BI102020S

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21-DE3 (MAGIC)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AROD, STM1358
	Mutation	:	YES
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	99287
	Strain	:	LT2
	Synonym	:	3-DEHYDROQUINASE, TYPE I DHQASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:213 , PHE A:225 , ALA A:233	BINDING SITE FOR RESIDUE CL A 253
2	AC2	SOFTWARE	HIS A:134 , HOH A:391 , HOH A:458 , HOH A:627 , HOH A:628	BINDING SITE FOR RESIDUE MG A 254
3	AC3	SOFTWARE	GLU A:217 , HOH A:279 , HOH A:300 , HOH A:427 , HOH A:690	BINDING SITE FOR RESIDUE MG A 255
4	AC4	SOFTWARE	HIS B:134 , HOH B:447 , HOH B:463 , HOH B:481 , HOH B:592 , HOH B:619	BINDING SITE FOR RESIDUE MG B 253
5	AC5	SOFTWARE	HOH B:259 , HOH B:281 , HOH B:379 , HOH B:419 , HOH B:457 , HOH B:621	BINDING SITE FOR RESIDUE MG B 254

(no "SS Bond" information available for 3O1N)

(no "Cis Peptide Bond" information available for 3O1N)

(no "SAP(SNP)/Variant" information available for 3O1N)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_I	PS01028	Dehydroquinase class I active site.	AROD_SALTY	114-144	2	A:114-144 B:114-144

(no "Exon" information available for 3O1N)

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:252
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    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  
           AROD_SALTY     1 MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3o1na_ A: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o1n A   1 MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGAISVADLRTVLTILHQA 252
                                    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

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    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  
           AROD_SALTY     1 MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3o1nb_ B: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------DHquinase_I-3o1nB01 B:19-247                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) ------------------DHquinase_I-3o1nB02 B:19-247                                                                                                                                                                                                         ----- Pfam domains (2)
         Sec.struct. author ...eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhh.......eee...------...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o1n B   1 MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAV------GAISVADLRTVLTILHQA 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       | -    |  240       250  
                                                                                                                                                                                                                                                             228    235

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: automated matches (113)

Protein domain: automated matches (113)

Salmonella enterica [TaxId: 99287] (5)

1a	d3o1na_	A:
1b	d3o1nb_	B:

(no "CATH Domain" information available for 3O1N)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DHquinase_I (17)

Salmonella typhimurium (7)

1a	DHquinase_I-3o1nB01	B:19-247
1b	DHquinase_I-3o1nB02	B:19-247

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AROD_SALTY | P58687)

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:0046279	3,4-dihydroxybenzoate biosynthetic process	The chemical reactions and pathways resulting in the formation of 3,4-dihydroxybenzoate.
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o1n)

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	3o1n
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	4.2.1.10
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UniProtKB/Swiss-Prot
	AROD_SALTY \| P58687	:	3l2i 3lb0 3m7w 3nnt 3oex 3s42 4gfs 4guf 4gug 4guh 4gui 4guj 4iuo

3l2i	CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2. RELATED ID: IDP90922 RELATED DB: TARGETDB
3lb0	CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2 WITH CITRATE BOUND TO THE ACTIVE SITE.
3m7w	CRYSTAL STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2 IN COVALENT COMPLEX WITH DEHYDROQUINATE.
3nnt	CRYSTAL STRUCTURE OF K170M MUTANT OF TYPE I 3- DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2 IN NON-COVALENT COMPLEX WITH DEHYDROQUINATE.

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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