1H0R - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   TYPE II DEHYDROQUINASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH 2,3-ANHYDRO-QUINIC ACID

Authors :   A. W. Roszak, D. A. Robinson, M. Frederickson, C. Abell, J. R. Coggins, A. J. Lapthorn

Date :   27 Jun 02 (Deposition) - 23 Oct 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (12x)

Keywords :   Dehydratase, Shikimate Pathway, Lyase, Aromatic Amino Acid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Robinson, A. W. Roszak, M. Frederickson, C. Abell, J. R. Coggins, A. J. Lapthorn
Structural Basis For Selectivity Of Oxime Based Inhibitors Towards Type Ii Dehydroquinase From Mycobacterium Tuberculosis
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
	Chains	:	A
	EC Number	:	4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MPET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET-15B
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	3-DEHYDROQUINASE, TYPE II DHQASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (12x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FA1	1	Ligand/Ion	2,3 -ANHYDRO-QUINIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 36)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FA1	12	Ligand/Ion	2,3 -ANHYDRO-QUINIC ACID
3	GOL	12	Ligand/Ion	GLYCEROL
4	PO4	12	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:54 , HOH A:2152 , HOH A:2153	BINDING SITE FOR RESIDUE PO4 A 201
2	AC2	SOFTWARE	ARG A:87 , ARG A:113 , HIS A:114	BINDING SITE FOR RESIDUE CL A 202
3	AC3	SOFTWARE	HIS A:106	BINDING SITE FOR RESIDUE CL A 203
4	AC4	SOFTWARE	TYR A:24 , ASN A:75 , GLY A:77 , GLY A:78 , HIS A:81 , ASP A:88 , HIS A:101 , ILE A:102 , SER A:103 , VAL A:105 , ARG A:112	BINDING SITE FOR RESIDUE FA1 A 200
5	AC5	SOFTWARE	TRP A:61 , GLN A:64 , HOH A:2078	BINDING SITE FOR RESIDUE GOL A 204

(no "SS Bond" information available for 1H0R)

(no "Cis Peptide Bond" information available for 1H0R)

(no "SAP(SNP)/Variant" information available for 1H0R)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_II	PS01029	Dehydroquinase class II signature.	AROQ_MYCBO	9-26	1	A:8-25
				AROQ_MYCTO	9-26	1	A:8-25
				AROQ_MYCTU	9-26	1	A:8-25

Biological Unit 1 (1, 36)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_II	PS01029	Dehydroquinase class II signature.	AROQ_MYCBO	9-26	12	A:8-25
				AROQ_MYCTO	9-26	12	A:8-25
				AROQ_MYCTU	9-26	12	A:8-25

(no "Exon" information available for 1H0R)

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:139
 aligned with AROQ_MYCBO | P0A4Z7 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
           AROQ_MYCBO     3 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d1h0ra_ A: Type I    I 3-dehydroquinate dehydratase                                                                                             SCOP domains
               CATH domains 1h0rA00 A:2-144      [code=3.40.50.9100, no name defined]                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..----.....hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh.....eeeee.......hhhhhh........eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h0r A   2 ELIVNVINGPNLGRLGR----VYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    11      |  - |      31        41        51        61        71        81        91       101       111       121       131       141   
                                           18   23

Chain A from PDB  Type:PROTEIN  Length:139
 aligned with AROQ_MYCTO | P9WPX6 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
           AROQ_MYCTO     3 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d1h0ra_ A: Type I    I 3-dehydroquinate dehydratase                                                                                             SCOP domains
               CATH domains 1h0rA00 A:2-144      [code=3.40.50.9100, no name defined]                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..----.....hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh.....eeeee.......hhhhhh........eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h0r A   2 ELIVNVINGPNLGRLGR----VYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    11      |  - |      31        41        51        61        71        81        91       101       111       121       131       141   
                                           18   23

Chain A from PDB  Type:PROTEIN  Length:139
 aligned with AROQ_MYCTU | P9WPX7 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
           AROQ_MYCTU     3 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d1h0ra_ A: Type I    I 3-dehydroquinate dehydratase                                                                                             SCOP domains
               CATH domains 1h0rA00 A:2-144      [code=3.40.50.9100, no name defined]                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..----.....hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh.....eeeee.......hhhhhh........eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h0r A   2 ELIVNVINGPNLGRLGR----VYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    11      |  - |      31        41        51        61        71        81        91       101       111       121       131       141   
                                           18   23

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: Flavodoxin-like (1057)

Superfamily: Type II 3-dehydroquinate dehydratase (40)

Family: Type II 3-dehydroquinate dehydratase (38)

Protein domain: Type II 3-dehydroquinate dehydratase (20)

Mycobacterium tuberculosis [TaxId: 1773] (11)

d1h0ra_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.9100, no name defined] (22)

Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. (3)

1h0rA00

A:2-144

(no "Pfam Domain" information available for 1H0R)

Asymmetric Unit(hide GO term definitions)

Chain A (AROQ_MYCBO | P0A4Z7)

molecular function
	GO:0003855	3-dehydroquinate dehydratase activity	Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
	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.

Chain A (AROQ_MYCTU | P9WPX7)

molecular function
	GO:0003855	3-dehydroquinate dehydratase activity	Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
	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.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A (AROQ_MYCTO | P9WPX6)

molecular function
	GO:0003855	3-dehydroquinate dehydratase activity	Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
	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 Unit
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(no "Cis Peptide Bonds" information available for 1h0r)

Biological Unit
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1h05	3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SULPHATE
1h0s	3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 3-HYDROXYIMINO-QUINIC ACID
2dhq	3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS

Description

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Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (7, 17)

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