1XAJ - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

Authors :   C. E. Nichols, J. Ren, K. Leslie, B. Dhaliwal, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers

Date :   25 Aug 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

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

Reference :   C. E. Nichols, J. Ren, K. Leslie, B. Dhaliwal, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Comparison Of Ligand Induced Conformational Changes And Domain Closure Mechanisms, Between Prokaryotic And Eukaryotic Dehydroquinate Synthases.
J. Mol. Biol. V. 343 533 2004
PubMed-ID: 15465043 | Reference-DOI: 10.1016/J.JMB.2004.08.039
(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	:	PMUT27
	Expression System Strain	:	BL21(DE3 PLYSS)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AROB
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	SADHQS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:178 , HIS A:242 , HIS A:256 , NAD A:400 , CRB A:500	BINDING SITE FOR RESIDUE ZN A 600
2	AC2	SOFTWARE	GLU B:178 , HIS B:242 , HIS B:256 , CRB B:501	BINDING SITE FOR RESIDUE ZN B 601
3	AC3	SOFTWARE	ASP A:39 , TYR A:41 , VAL A:42 , TYR A:45 , GLY A:67 , GLU A:68 , LYS A:71 , GLY A:99 , GLY A:100 , ALA A:101 , ASP A:104 , THR A:124 , THR A:125 , LEU A:127 , ASP A:130 , SER A:131 , LYS A:136 , LYS A:145 , ASN A:146 , PHE A:163 , THR A:166 , LEU A:167 , GLN A:171 , CRB A:500 , ZN A:600 , HOH A:605 , HOH A:609 , HOH A:610 , HOH A:613 , HOH A:618 , HOH A:699 , GLN B:286	BINDING SITE FOR RESIDUE NAD A 400
4	AC4	SOFTWARE	GLN A:286 , ASP B:39 , TYR B:41 , VAL B:42 , TYR B:45 , GLY B:67 , GLU B:68 , LYS B:71 , GLY B:100 , ALA B:101 , ASP B:104 , THR B:124 , THR B:125 , LEU B:127 , ASP B:130 , SER B:131 , LYS B:136 , LYS B:145 , ASN B:146 , PHE B:163 , THR B:166 , LEU B:167 , GLN B:171 , LYS B:221 , CRB B:501 , HOH B:1014 , HOH B:1017 , HOH B:1018 , HOH B:1022 , HOH B:1027 , HOH B:1056	BINDING SITE FOR RESIDUE NAD B 401
5	AC5	SOFTWARE	ASP A:130 , LYS A:136 , ASN A:146 , GLU A:178 , LYS A:181 , LYS A:221 , ARG A:235 , LEU A:238 , ASN A:239 , HIS A:242 , HIS A:246 , HIS A:256 , LYS A:314 , NAD A:400 , ZN A:600 , HOH A:610 , ARG B:115	BINDING SITE FOR RESIDUE CRB A 500
6	AC6	SOFTWARE	ARG A:115 , ASP B:130 , LYS B:136 , ASN B:146 , GLU B:178 , LYS B:181 , LYS B:221 , ARG B:235 , LEU B:238 , ASN B:239 , HIS B:242 , HIS B:246 , HIS B:256 , LYS B:314 , NAD B:401 , ZN B:601 , HOH B:1018	BINDING SITE FOR RESIDUE CRB B 501

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

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

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

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

(no "Exon" information available for 1XAJ)

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:337
 aligned with AROB_STAAR | Q6GGU4 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:352
                                    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       260       270       280       290       300       310       320       330       340       350  
           AROB_STAAR     1 MKLQTTYPSNNYPIFVEHGAIDHISTYIDQFDQSFILIDEHVNQYFADKFNDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFEQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLKGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDINHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLIRQFGDIVVQHVDQLTLQHACEQLKTY 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xajA01 A:1-166  [code=3.40.50.1970, no name defined]                                                                                                                 -----------------------------------------------------------------------------------------------------------------------------------           -------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeee.hhhhhhhhhhh....eeeeeehhhhhhhh......----.eeeeee.hhhhh.hhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhh.eeeeee...hhhhhh...eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....-----------.................eee..ee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xaj A   1 MKLQTTYPSNNYPIYVEHGAIKYIGTYLNQFDQSFLLIDEYVNQYFANKFDDI----NVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFKQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLNGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDISHYIQYLIQLGYPLDM-----------YMLSDKKNDKQGVQMVLMRQFGDIVVQHVDQLTLQHACEQLKTY 352
                                    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       260       270       280       290      |  -       310       320       330       340       350  
                                                                               53   58                                                                                                                                                                                                                                            297         309

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with AROB_STAAR | Q6GGU4 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:352
                                    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       260       270       280       290       300       310       320       330       340       350  
           AROB_STAAR     1 MKLQTTYPSNNYPIFVEHGAIDHISTYIDQFDQSFILIDEHVNQYFADKFNDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFEQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLKGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDINHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLIRQFGDIVVQHVDQLTLQHACEQLKTY 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xajB01 B:1-166  [code=3.40.50.1970, no name defined]                                                                                                                 -----------------------------------------------------------------------------------------------------------------------------------           -------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------    ---DHQ_synthase-1xajB01 B:61-317                                                                                                                                                                                                                                    ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------    ---DHQ_synthase-1xajB02 B:61-317                                                                                                                                                                                                                                    ----------------------------------- Pfam domains (2)
         Sec.struct. author .eee........eeeee.hhhhhhhhhhh....eeeeeehhhhhhhh......----.eeeeee.hhhhh.hhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhh.eeeeee...hhhhhh...eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....-----------.................eee..ee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xaj B   1 MKLQTTYPSNNYPIYVEHGAIKYIGTYLNQFDQSFLLIDEYVNQYFANKFDDI----NVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFKQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLNGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDISHYIQYLIQLGYPLDM-----------YMLSDKKNDKQGVQMVLMRQFGDIVVQHVDQLTLQHACEQLKTY 352
                                    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       260       270       280       290      |  -       310       320       330       340       350  
                                                                               53   58                                                                                                                                                                                                                                            297         309

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 '\|'

(no "SCOP Domain" information available for 1XAJ)

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=3.40.50.1970, no name defined] (28)

Staphylococcus aureus. Organism_taxid: 1280. (5)

1a	1xajA01	A:1-166
1b	1xajB01	B:1-166

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHQS (27)

Family: DHQ_synthase (15)

Staphylococcus aureus (strain MRSA252) (5)

1a	DHQ_synthase-1xajB01	B:61-317
1b	DHQ_synthase-1xajB02	B:61-317

Asymmetric Unit(hide GO term definitions)

Chain A,B (AROB_STAAR | Q6GGU4)

molecular function
	GO:0003856	3-dehydroquinate synthase activity	Catalysis of the reaction: 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate.
	GO:0016838	carbon-oxygen lyase activity, acting on phosphates	Catalysis of the cleavage of a carbon-oxygen bond by elimination of a phosphate.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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Biological Units
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	1xaj
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	4.2.3.4
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UniProtKB/Swiss-Prot
	AROB_STAAR \| Q6GGU4	:	1xag 1xah 1xai 1xal

1nr5	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH COFACTOR AND SUBSTRATE ANALOGUE
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
1nvb	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH SUBSTRATE ANALOGUE
1nvd	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM B, CLOSED FORM WITH SUBSTRATE ANALOGUE
1nve	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD+, CRYSTAL FORM E, OPEN FORM WITH CO-FACTOR
1nvf	CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, ADP AND CBP, CRYSTAL FORM H, CLOSED FORM WITH CO-FACTOR ANALOGUE AND SUBSTRATE ANALOGUE
1xag	CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CAR
1xah	CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE
1xai	CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE
1xal	CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE (SOAK)

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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