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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM WITH CLOSE LOOP CONFORMATION.

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

Date :   13 Aug 10 (Deposition) - 01 Sep 10 (Release) - 04 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, 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, C, D
	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	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AROD, STM1358
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	90371
	Strain	:	LT2
	Synonym	:	3-DEHYDROQUINASE, TYPE I DHQASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

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

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:213 , ALA A:233 , GLN A:236 , HOH A:354	BINDING SITE FOR RESIDUE CL A 253
2	AC2	SOFTWARE	ARG B:213 , ALA B:233 , GLN B:236	BINDING SITE FOR RESIDUE CL B 253
3	AC3	SOFTWARE	ARG C:213 , ALA C:233 , GLN C:236 , HOH C:324	BINDING SITE FOR RESIDUE CL C 253
4	AC4	SOFTWARE	ARG D:213 , ALA D:233 , GLN D:236 , HOH D:774	BINDING SITE FOR RESIDUE CL D 253

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_I	PS01028	Dehydroquinase class I active site.	AROD_SALTY	114-144	4	A:114-144 B:114-144 C:114-144 D:114-144

Biological Unit 1 (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 - -

Biological Unit 2 (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	- - C:114-144 D:114-144

(no "Exon" information available for 3OEX)

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:251
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           AROD_SALTY     2 KTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3oexa_ 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
                 3oex A   2 KTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:253
                             1                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
           AROD_SALTY     - -MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3oexb_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oex B   0 AMKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

Chain C from PDB  Type:PROTEIN  Length:251
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           AROD_SALTY     2 KTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3oexc_ C: 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..eeeeeee......hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: C:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oex C   2 KTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain D from PDB  Type:PROTEIN  Length:251
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           AROD_SALTY     2 KTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3oexd_ D: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------DHquinase_I-3oexD01 D:19-247                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) -----------------DHquinase_I-3oexD02 D:19-247                                                                                                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) -----------------DHquinase_I-3oexD03 D:19-247                                                                                                                                                                                                         ----- Pfam domains (3)
           Pfam domains (4) -----------------DHquinase_I-3oexD04 D:19-247                                                                                                                                                                                                         ----- Pfam domains (4)
         Sec.struct. author ..eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: D:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oex D   2 KTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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 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: automated matches (54)

Salmonella typhimurium [TaxId: 90371] (5)

1a	d3oexa_	A:
1b	d3oexb_	B:
1c	d3oexc_	C:
1d	d3oexd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DHquinase_I (17)

Salmonella typhimurium (7)

1a	DHquinase_I-3oexD01	D:19-247
1b	DHquinase_I-3oexD02	D:19-247
1c	DHquinase_I-3oexD03	D:19-247
1d	DHquinase_I-3oexD04	D:19-247

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

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	AROD_SALTY \| P58687	:	3l2i 3lb0 3m7w 3nnt 3o1n 3s42 4gfs 4guf 4gug 4guh 4gui 4guj 4iuo

3l2i	1.85 ANGSTROM CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2
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
3o1n	1.03 ANGSTROM CRYSTAL STRUCTURE OF Q236A MUTANT TYPE I DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM RELATED ID: IDP90922 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (1, 4)

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SS Bonds (0, 0)

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