1NVB - JenaLib

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Title :   CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE

Authors :   C. E. Nichols, J. Ren, H. K. Lamb, A. R. Hawkins, D. K. Stammers

Date :   03 Feb 03 (Deposition) - 18 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Shikimate Pathway, Aromatic Amino Acid Biosynthesis, Dhqs, Closed Form, Form C, Domain Movement, Cyclase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Nichols, J. Ren, H. K. Lamb, A. R. Hawkins, D. K. Stammers
Ligand-Induced Conformational Changes And A Mechanism For Domain Closure In Aspergillus Nidulans Dehydroquinate Synthase
J. Mol. Biol. V. 327 129 2003
PubMed-ID: 12614613 | Reference-DOI: 10.1016/S0022-2836(03)00086-X
(for further references see the PDB file header)

Molecule 1 - 3-DEHYDROQUINATE SYNTHASE
	Chains	:	A, B
	EC Number	:	4.2.3.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTR51
	Expression System Strain	:	GLW38 (AROB-)
	Expression System Taxid	:	562
	Expression System Vector	:	PTRC99A
	Expression System Vector Type	:	PLASMID
	Gene	:	AROMA
	Organism Scientific	:	EMERICELLA NIDULANS
	Organism Taxid	:	162425
	Synonym	:	DHQS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	CRB	2	Ligand/Ion	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
3	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CRB	2	Ligand/Ion	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CRB	2	Ligand/Ion	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
3	NAD	-1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:146 , GLU A:194 , HIS A:271 , HIS A:287 , NAD A:400 , CRB A:500	BINDING SITE FOR RESIDUE ZN A 600
2	AC2	SOFTWARE	ASP B:146 , GLU B:194 , HIS B:271 , HIS B:287 , CRB B:501	BINDING SITE FOR RESIDUE ZN B 601
3	AC3	SOFTWARE	VAL A:185	BINDING SITE FOR RESIDUE CL A 604
4	AC4	SOFTWARE	ARG A:105 , MET A:129 , GLY A:131 , HOH A:665	BINDING SITE FOR RESIDUE CL A 605
5	AC5	SOFTWARE	ASP A:44 , ASN A:46 , ILE A:47 , GLU A:81 , LYS A:84 , GLY A:114 , GLY A:115 , VAL A:116 , ASP A:119 , THR A:139 , THR A:140 , LEU A:142 , ASP A:146 , SER A:147 , LYS A:152 , LYS A:161 , ASN A:162 , PHE A:179 , THR A:182 , LEU A:183 , PRO A:184 , GLU A:187 , ASN A:190 , GLU A:194 , HIS A:287 , CRB A:500 , ZN A:600 , HOH A:709 , GLY B:340	BINDING SITE FOR RESIDUE NAD A 400
6	AC6	SOFTWARE	ARG A:130 , ASP A:146 , LYS A:152 , ASN A:162 , GLU A:194 , LYS A:197 , LYS A:250 , ARG A:264 , LEU A:267 , ASN A:268 , HIS A:271 , HIS A:275 , HIS A:287 , LYS A:356 , NAD A:400 , ZN A:600	BINDING SITE FOR RESIDUE CRB A 500
7	AC7	SOFTWARE	ARG B:130 , ASP B:146 , LYS B:152 , ASN B:162 , GLU B:194 , LYS B:197 , LYS B:250 , ARG B:264 , LEU B:267 , ASN B:268 , HIS B:271 , HIS B:275 , HIS B:287 , LYS B:356 , ZN B:601 , HOH B:660	BINDING SITE FOR RESIDUE CRB B 501

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

Asymmetric Unit

No.	Residues
1	Thr A:67	-	Pro A:68
2	Asn A:100	-	Pro A:101
3	Thr A:282	-	Pro A:283
4	Asn B:3	-	Pro B:4
5	Thr B:67	-	Pro B:68
6	Asn B:100	-	Pro B:101
7	Thr B:282	-	Pro B:283

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

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

(no "Exon" information available for 1NVB)

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:390
 aligned with ARO1_EMENI | P07547 from UniProtKB/Swiss-Prot  Length:1583

    Alignment length:390
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
           ARO1_EMENI     3 NPTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKAAAEITPSPRLLIYNAPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVRPGEHRFEGIEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLA 392
               SCOP domains d1nvba_ A: Dehydroquinate synthase, DHQS                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -1nvbA01 A:4-182  [code=3.40.50.1970, no name defined]                                                                                                                              1nvbA02 A:183-391 Dehydroquinate synthase-like - alpha domain                                                                                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.......eeee......hhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhhhh........ee..eee..ee.....ee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nvb A   3 NPTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKRAAEITPSPRLLIYNRPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVTPGEHRFEGTEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLA 392
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392

Chain B from PDB  Type:PROTEIN  Length:391
 aligned with ARO1_EMENI | P07547 from UniProtKB/Swiss-Prot  Length:1583

    Alignment length:391
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392 
           ARO1_EMENI     3 NPTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKAAAEITPSPRLLIYNAPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVRPGEHRFEGIEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP 393
               SCOP domains d1nvbb_ B: Dehydroquinate synthase, DHQS                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -1nvbB01 B:4-182  [code=3.40.50.1970, no name defined]                                                                                                                              1nvbB02 B:183-391 Dehydroquinate synthase-like - alpha domain                                                                                                                                                    -- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------DHQ_synthase-1nvbB01 B:74-359                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------DHQ_synthase-1nvbB02 B:74-359                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (2)
         Sec.struct. author ..eee.......eeee......hhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhh.....hhhhhhhhhhhh........ee..eee..ee.....ee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nvb B   3 NPTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKRAAEITPSPRLLIYNRPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVTPGEHRFEGTEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP 393
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: Multi-domain proteins (alpha and beta) (2421)

Fold: Dehydroquinate synthase-like (30)

Superfamily: Dehydroquinate synthase-like (30)

Family: Dehydroquinate synthase, DHQS (11)

Protein domain: Dehydroquinate synthase, DHQS (11)

Emericella nidulans (Aspergillus nidulans) [TaxId: 162425] (10)

1a	d1nvba_	A:
1b	d1nvbb_	B:

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHQS (27)

Family: DHQ_synthase (15)

Emericella nidulans (Aspergillus nidulans) (9)

1a	DHQ_synthase-1nvbB01	B:74-359
1b	DHQ_synthase-1nvbB02	B:74-359

Asymmetric Unit(hide GO term definitions)

Chain A,B (ARO1_EMENI | P07547)

molecular function
	GO:0003855	3-dehydroquinate dehydratase activity	Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
	GO:0003856	3-dehydroquinate synthase activity	Catalysis of the reaction: 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate.
	GO:0003866	3-phosphoshikimate 1-carboxyvinyltransferase activity	Catalysis of the reaction: 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004764	shikimate 3-dehydrogenase (NADP+) activity	Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
	GO:0004765	shikimate kinase activity	Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	ARO1_EMENI \| P07547	:	1dqs 1nr5 1nrx 1nua 1nva 1nvd 1nve 1nvf 1sg6

1nr5	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH COFACTOR
1nrx	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD, CRYSTAL FORM F, OPEN FORM WITH COFACTOR
1nua	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, APO, CRYSTAL FORM D, OPEN FORM
1nva	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND ADP, CRYSTAL FORM D, OPEN FORM WITH CO-FACTOR ANALOGUE
1nvd	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM B, CLOSED FORM WITH SUBSTRATE ANALOGUE AND REDUCED COFACTOR
1nve	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD, CRYSTAL FORM E, OPEN FORM WITH COFACTOR
1nvf	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, ADP AND CARBAPHOSPHONATE, CRYSTAL FORM H, CLOSED FORM WITH CO-FACTOR ANALOGUE AND SUBSTRATE ANALOGUE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (21, 21)

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