4B6R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE INHIBITED BY (2S)-2-(4-METHOXY)BENZYL-3-DEHYDROQUINIC ACID

Authors :   J. M. Otero, A. L. Llamas-Saiz, E. Lence, L. Tizon, A. Peon, V. F. V. Praze H. Lamb, A. R. Hawkins, C. Gonzalez-Bello, M. J. Van Raaij

Date :   14 Aug 12 (Deposition) - 19 Dec 12 (Release) - 17 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Lence, L. Tizon, J. M. Otero, A. Peon, V. F. V. Prazeres, A. L. Llamas-Saiz, M. J. Van Raaij, H. Lamb, A. R. Hawkins, C. Gonzalez-Bello
Mechanistic Basis Of The Inhibition Of Type Ii Dehydroquinase By (2S)- And (2R)-2-Benzyl-3-Dehydroquinic Acids.
Acs Chem. Biol. V. 8 568 2013
PubMed-ID: 23198883 | Reference-DOI: 10.1021/CB300493S

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
	Chains	:	A, B, C
	EC Number	:	4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HELICOBACTER PYLORI 26695
	Organism Taxid	:	85962
	Synonym	:	3-DEHYDROQUINASE, TYPE II DHQASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	3DQ	3	Ligand/Ion	(1R,2S,4S,5R)-2-(4-METHOXYPHENYL)METHYL-1,4,5-TRIHYDROXY-3-OXOCYCLOHEXANE-1-CARBOXYLICACID
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , MET A:13 , TYR A:22 , ASN A:76 , GLY A:78 , ALA A:79 , HIS A:82 , HIS A:102 , LEU A:103 , THR A:104 , ARG A:113 , HOH A:2004 , ASP C:89 , LEU C:93	BINDING SITE FOR RESIDUE 3DQ A1158
2	AC2	SOFTWARE	ASP A:89 , LEU A:93 , HOH A:2052 , ASN B:10 , LEU B:14 , ARG B:17 , TYR B:22 , ASN B:76 , GLY B:78 , ALA B:79 , HIS B:82 , HIS B:102 , LEU B:103 , THR B:104 , ARG B:113	BINDING SITE FOR RESIDUE 3DQ B1158
3	AC3	SOFTWARE	ASP B:89 , LEU B:93 , HOH B:2032 , ASN C:10 , ARG C:17 , TYR C:22 , ASN C:76 , GLY C:78 , ALA C:79 , HIS C:82 , HIS C:102 , LEU C:103 , THR C:104 , ARG C:113	BINDING SITE FOR RESIDUE 3DQ C1158
4	AC4	SOFTWARE	GLU A:57 , PHE B:54 , GLU B:57 , GLU C:57	BINDING SITE FOR RESIDUE SO4 B1159

(no "SS Bond" information available for 4B6R)

(no "Cis Peptide Bond" information available for 4B6R)

(no "SAP(SNP)/Variant" information available for 4B6R)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_II	PS01029	Dehydroquinase class II signature.	AROQ_HELPY	6-23	3	A:6-23 B:6-23 C:6-23

(no "Exon" information available for 4B6R)

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:157
 aligned with AROQ_HELPY | Q48255 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           AROQ_HELPY     1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKN 157
               SCOP domains d4b6ra_ A: Type II 3-dehydroquinate dehydratase                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh...........hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh....eeeee.......hhhhh.hhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6r A   1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKN 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with AROQ_HELPY | Q48255 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           AROQ_HELPY     1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKN 157
               SCOP domains d4b6rb_ B: Type II 3-dehydroquinate dehydratase                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh...........hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh....eeeee.......hhhhh.hhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6r B   1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKN 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with AROQ_HELPY | Q48255 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           AROQ_HELPY     1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKN 157
               SCOP domains d4b6rc_ C: Type II 3-dehydroquinate dehydratase                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh...........hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh...eeeee.......hhhhh.hhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6r C   1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKN 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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: 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)

Helicobacter pylori [TaxId: 85962] (2)

1a	d4b6ra_	A:
1b	d4b6rb_	B:
1c	d4b6rc_	C:

(no "CATH Domain" information available for 4B6R)

(no "Pfam Domain" information available for 4B6R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (AROQ_HELPY | Q48255)

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/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
		3DQ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4b6r)

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)

Access by PDB/NDB ID
	4b6r
		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
	AROQ_HELPY \| Q48255
		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)
	4.2.1.10
		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

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
	AROQ_HELPY \| Q48255
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	AROQ_HELPY \| Q48255	:	1j2y 2c4v 2c4w 2c57 2wks 2xb9 2xd9 2xda 4b6s

1j2y	CRYSTAL STRUCTURE OF THE TYPE II 3-DEHYDROQUINASE
2c4v	H. PYLORI TYPE II DHQASE IN COMPLEX WITH CITRATE
2c4w	TYPE II DEHYDROQUINASE FROM H. PYLORI IN COMPLEX WITH AH9095
2c57	H.PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH FA1
2wks	STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE WITH A NEW CARBASUGAR-THIOPHENE INHIBITOR.
2xb9	STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (2R)-2-(4- METHOXYBENZYL)-3-DEHYDROQUINIC ACID
2xd9	STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6, 7-TRIHYDROXY-2-((E)-PROP-1-ENYL)-4,5,6,7- TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID
2xda	STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2- CYCLOPROPYL)ETHYL-4,6,7-TRIHYDROXY-4,5,6,7- TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID
4b6o	STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE INHIBITED BY (2S)-2-(4-METHOXY)BENZYL-3 -DEHYDROQUINIC ACID
4b6p	STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE INHIBITED BY (2S)-2-PERFLUOROBENZYL-3- DEHYDROQUINIC ACID
4b6q	STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE INHIBITED BY (2R)-2-(BENZOTHIOPHEN-5-YL) METHYL-3-DEHYDROQUINIC ACID
4b6s	STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE INHIBITED BY (2S)-2-PERFLUOROBENZYL-3- DEHYDROQUINIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File