Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3M7W

Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Covalent Complex with Dehydroquinate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003855	molecular_function	3-dehydroquinate dehydratase activity
A	0005829	cellular_component	cytosol
A	0008652	biological_process	amino acid biosynthetic process
A	0009073	biological_process	aromatic amino acid family biosynthetic process
A	0009423	biological_process	chorismate biosynthetic process
A	0016829	molecular_function	lyase activity
A	0046279	biological_process	3,4-dihydroxybenzoate biosynthetic process
B	0003855	molecular_function	3-dehydroquinate dehydratase activity
B	0005829	cellular_component	cytosol
B	0008652	biological_process	amino acid biosynthetic process
B	0009073	biological_process	aromatic amino acid family biosynthetic process
B	0009423	biological_process	chorismate biosynthetic process
B	0016829	molecular_function	lyase activity
B	0046279	biological_process	3,4-dihydroxybenzoate biosynthetic process
C	0003855	molecular_function	3-dehydroquinate dehydratase activity
C	0005829	cellular_component	cytosol
C	0008652	biological_process	amino acid biosynthetic process
C	0009073	biological_process	aromatic amino acid family biosynthetic process
C	0009423	biological_process	chorismate biosynthetic process
C	0016829	molecular_function	lyase activity
C	0046279	biological_process	3,4-dihydroxybenzoate biosynthetic process
D	0003855	molecular_function	3-dehydroquinate dehydratase activity
D	0005829	cellular_component	cytosol
D	0008652	biological_process	amino acid biosynthetic process
D	0009073	biological_process	aromatic amino acid family biosynthetic process
D	0009423	biological_process	chorismate biosynthetic process
D	0016829	molecular_function	lyase activity
D	0046279	biological_process	3,4-dihydroxybenzoate biosynthetic process
E	0003855	molecular_function	3-dehydroquinate dehydratase activity
E	0005829	cellular_component	cytosol
E	0008652	biological_process	amino acid biosynthetic process
E	0009073	biological_process	aromatic amino acid family biosynthetic process
E	0009423	biological_process	chorismate biosynthetic process
E	0016829	molecular_function	lyase activity
E	0046279	biological_process	3,4-dihydroxybenzoate biosynthetic process
F	0003855	molecular_function	3-dehydroquinate dehydratase activity
F	0005829	cellular_component	cytosol
F	0008652	biological_process	amino acid biosynthetic process
F	0009073	biological_process	aromatic amino acid family biosynthetic process
F	0009423	biological_process	chorismate biosynthetic process
F	0016829	molecular_function	lyase activity
F	0046279	biological_process	3,4-dihydroxybenzoate biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DQA A 253

Chain	Residue
A	SER21
A	PHE225
A	SER232
A	ALA233
A	GLN236
A	GLU46
A	ARG48
A	ARG82
A	HIS143
A	LYS170
A	MET203
A	MET205
A	ARG213

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 254

Chain	Residue
A	ALA15
A	ARG243
A	THR247
A	HIS250
A	HOH1011

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DQA B 253

Chain	Residue
B	SER21
B	GLU46
B	ARG48
B	ARG82
B	HIS143
B	LYS170
B	ARG213
B	PHE225
B	SER232
B	ALA233
B	GLN236

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 254

Chain	Residue
B	ALA15
B	ARG243
B	THR247

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 255

Chain	Residue
B	GLY87
B	PHE145
B	HOH285
B	HOH587
B	HOH659
D	GLY87
D	PHE145
D	PRO234

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DQA C 253

Chain	Residue
C	SER21
C	GLU46
C	ARG48
C	ARG82
C	HIS143
C	LYS170
C	MET203
C	ARG213
C	PHE225
C	SER232
C	ALA233
C	GLN236

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL C 254

Chain	Residue
C	SER83
C	LYS85
C	LEU92
C	TYR97
C	HOH286
C	HOH304
C	HOH445
C	HOH756

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL C 255

Chain	Residue
C	GLY87
C	PHE145
C	PRO234
C	HOH444
C	HOH544
C	HOH588
F	GLY87
F	PHE145

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 256

Chain	Residue
C	ALA15
C	ARG243
C	THR247

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 257

Chain	Residue
B	GLU193
C	THR177
C	LYS178
C	HOH259
C	HOH598
C	HOH1094
F	THR93

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DQA D 253

Chain	Residue
D	SER21
D	GLU46
D	ARG48
D	ARG82
D	HIS143
D	LYS170
D	MET205
D	ARG213
D	PHE225
D	SER232
D	ALA233
D	GLN236

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL D 254

Chain	Residue
D	SER83
D	LYS85
D	LEU92
D	TYR97
D	HOH282
D	HOH304
D	HOH357
D	HOH901

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL D 255

Chain	Residue
D	GLY108
D	VAL110
D	ASP111
D	ASN135
D	HOH574
D	ARG69

site_id	BC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DQA E 253

Chain	Residue
E	SER21
E	GLU46
E	ARG48
E	ARG82
E	HIS143
E	LYS170
E	ARG213
E	PHE225
E	SER232
E	ALA233
E	GLN236

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 254

Chain	Residue
D	ASN135
E	THR5
E	HIS132
E	ASN135
E	ASP167
E	HOH1063

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 255

Chain	Residue
E	SER83
E	LEU92
E	TYR97
E	HOH309
E	HOH327
E	HOH464

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 256

Chain	Residue
E	GLU33
E	LYS229
E	LYS230
F	ASP121
F	ASP122
F	HOH558
F	HOH729

site_id	BC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DQA F 253

Chain	Residue
F	SER21
F	GLU46
F	ARG48
F	ARG82
F	HIS143
F	LYS170
F	MET203
F	ARG213
F	PHE225
F	SER232
F	ALA233
F	GLN236

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL F 254

Chain	Residue
F	LYS147
F	THR148
F	GLN176
F	ASP180
F	HOH397
F	HOH816

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL F 255

Chain	Residue
A	ALA53
F	GLU217
F	HIS250
F	HOH976

Functional Information from PROSITE/UniProt

site_id	PS01028
Number of Residues	31
Details	DEHYDROQUINASE_I Dehydroquinase class I active site. DLELftgddevkatvgyahqhnvaVImSNHD

Chain	Residue	Details
A	ASP114-ASP144

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23341204","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24437575","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site.","authors":["Minasov G.","Light S.H.","Shuvalova L.","Papazisi L.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"AUG-2012","submissionDatabase":"PDB data bank","title":"1.8 angstrom crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with nickel bound at active site.","authors":["Light S.H.","Minasov G.","Krishna S.N.","Shuvalova L.","Kwon K.","Lavie A.","Anderson W.F."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Active site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23341204","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site.","authors":["Minasov G.","Light S.H.","Shuvalova L.","Papazisi L.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella enterica typhimurium LT2 with malonate and boric acid at the active site.","authors":["Light S.H.","Minasov G.","Duban M.-E.","Halavaty A.S.","Krishna S.N.","Shuvalova L.","Kwon K.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"AUG-2012","submissionDatabase":"PDB data bank","title":"1.8 angstrom crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with nickel bound at active site.","authors":["Light S.H.","Minasov G.","Krishna S.N.","Shuvalova L.","Kwon K.","Lavie A.","Anderson W.F."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24437575","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site.","authors":["Minasov G.","Light S.H.","Shuvalova L.","Papazisi L.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella enterica typhimurium LT2 with malonate and boric acid at the active site.","authors":["Light S.H.","Minasov G.","Duban M.-E.","Halavaty A.S.","Krishna S.N.","Shuvalova L.","Kwon K.","Anderson W.F."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23341204","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24437575","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site.","authors":["Minasov G.","Light S.H.","Shuvalova L.","Papazisi L.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella enterica typhimurium LT2 with malonate and boric acid at the active site.","authors":["Light S.H.","Minasov G.","Duban M.-E.","Halavaty A.S.","Krishna S.N.","Shuvalova L.","Kwon K.","Anderson W.F."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23341204","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24437575","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site.","authors":["Minasov G.","Light S.H.","Shuvalova L.","Papazisi L.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella enterica typhimurium LT2 with malonate and boric acid at the active site.","authors":["Light S.H.","Minasov G.","Duban M.-E.","Halavaty A.S.","Krishna S.N.","Shuvalova L.","Kwon K.","Anderson W.F."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"AUG-2012","submissionDatabase":"PDB data bank","title":"1.8 angstrom crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with nickel bound at active site.","authors":["Light S.H.","Minasov G.","Krishna S.N.","Shuvalova L.","Kwon K.","Lavie A.","Anderson W.F."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24437575","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site.","authors":["Minasov G.","Light S.H.","Shuvalova L.","Papazisi L.","Anderson W.F."]}}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)