Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4K1W

Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and d-mannonate

Replaces: 3R4E

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0008927	molecular_function	mannonate dehydratase activity
A	0009063	biological_process	amino acid catabolic process
A	0016052	biological_process	carbohydrate catabolic process
A	0016829	molecular_function	lyase activity
A	0046872	molecular_function	metal ion binding
B	0000287	molecular_function	magnesium ion binding
B	0008927	molecular_function	mannonate dehydratase activity
B	0009063	biological_process	amino acid catabolic process
B	0016052	biological_process	carbohydrate catabolic process
B	0016829	molecular_function	lyase activity
B	0046872	molecular_function	metal ion binding
C	0000287	molecular_function	magnesium ion binding
C	0008927	molecular_function	mannonate dehydratase activity
C	0009063	biological_process	amino acid catabolic process
C	0016052	biological_process	carbohydrate catabolic process
C	0016829	molecular_function	lyase activity
C	0046872	molecular_function	metal ion binding
D	0000287	molecular_function	magnesium ion binding
D	0008927	molecular_function	mannonate dehydratase activity
D	0009063	biological_process	amino acid catabolic process
D	0016052	biological_process	carbohydrate catabolic process
D	0016829	molecular_function	lyase activity
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 501

Chain	Residue
A	ASP210
A	GLU236
A	GLU262
A	CS2502
A	HOH848

site_id	AC2
Number of Residues	19
Details	BINDING SITE FOR RESIDUE CS2 A 502

Chain	Residue
A	HIS212
A	GLU236
A	GLU262
A	ARG283
A	HIS312
A	PRO314
A	ASP316
A	GLU339
A	LEU389
A	TRP402
A	MG501
A	HOH634
A	HOH848
B	TYR75
B	TRP76
A	ASN37
A	HIS122
A	ARG147
A	ASP210

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE A 503

Chain	Residue
A	LYS192
A	GLU195
A	MET226
A	TYR230

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE CO2 A 504

Chain	Residue
A	ARG78
A	GLY79
A	PRO80
A	VAL81
A	THR82
B	GLY79
B	PRO80
B	VAL81
B	THR82

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CO2 A 505

Chain	Residue
A	GLU228
A	PRO229
A	GLN231
A	HOH859
C	HOH718

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PDO A 506

Chain	Residue
A	HIS209
A	ASP210
A	TYR215
A	HOH758

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 501

Chain	Residue
B	ASP210
B	GLU236
B	GLU262
B	CS2502
B	HOH856

site_id	AC8
Number of Residues	19
Details	BINDING SITE FOR RESIDUE CS2 B 502

Chain	Residue
A	TYR75
A	TRP76
B	ASN37
B	HIS122
B	ARG147
B	ASP210
B	HIS212
B	GLU236
B	GLU262
B	ARG283
B	HIS312
B	PRO314
B	ASP316
B	GLU339
B	LEU389
B	TRP402
B	MG501
B	HOH625
B	HOH856

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PGE B 503

Chain	Residue
B	PRO191
B	LYS192
B	GLU195
B	TYR230
D	PHE203

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG B 504

Chain	Residue
B	HOH874
B	HOH882
B	HOH883
D	HOH812

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PDO B 505

Chain	Residue
B	HIS209
B	ASP210
B	GLY211
B	TYR215
B	HOH745

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 501

Chain	Residue
C	ASP210
C	GLU236
C	GLU262
C	CS2502
C	HOH812

site_id	BC4
Number of Residues	19
Details	BINDING SITE FOR RESIDUE CS2 C 502

Chain	Residue
C	ASP316
C	GLU339
C	LEU389
C	TRP402
C	MG501
C	HOH613
C	HOH812
D	TYR75
D	TRP76
C	ASN37
C	HIS122
C	ARG147
C	ASP210
C	HIS212
C	GLU236
C	GLU262
C	ARG283
C	HIS312
C	PRO314

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE C 503

Chain	Residue
C	PRO191
C	LYS192
C	GLU195
C	TYR230

site_id	BC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE CO2 C 504

Chain	Residue
C	ARG78
C	GLY79
C	PRO80
C	VAL81
C	THR82
D	GLY79
D	PRO80
D	VAL81
D	THR82

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CO2 C 505

Chain	Residue
C	ARG297
C	ALA299
C	ASP300
C	SER303
C	PRO333
C	ASN334

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CO3 C 506

Chain	Residue
C	ARG61
C	MET103
C	HOH682
C	HOH776

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PDO C 507

Chain	Residue
C	TRP181
C	HIS209
C	ASP210
C	TYR215

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 501

Chain	Residue
D	ASP210
D	GLU236
D	GLU262
D	CS2502
D	HOH801

site_id	CC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE CS2 D 502

Chain	Residue
C	TYR75
D	ASN37
D	HIS122
D	ARG147
D	ASP210
D	HIS212
D	GLU236
D	GLU262
D	ARG283
D	HIS312
D	PRO314
D	ASP316
D	GLU339
D	LEU389
D	TRP402
D	MG501
D	HOH621
D	HOH801

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE D 503

Chain	Residue
D	ASN188
D	LYS192
D	GLU195
D	TYR230

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CO2 D 504

Chain	Residue
C	GLU245
C	HOH612
D	LYS271
D	ASP272
D	HOH637
D	HOH707
D	HOH820

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PDO D 505

Chain	Residue
D	HIS209
D	GLY211
D	TYR215

Functional Information from PROSITE/UniProt

site_id	PS00908
Number of Residues	26
Details	MR_MLE_1 Mandelate racemase / muconate lactonizing enzyme family signature 1. AiAAVDmALwDIkAKmagmPLyqLLG

Chain	Residue	Details
A	ALA85-GLY110

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton donor/acceptor => ECO:0000305\|PubMed:17944491

Chain	Residue	Details
A	TYR159
A	HIS212
B	TYR159
B	HIS212
C	TYR159
C	HIS212
D	TYR159
D	HIS212

site_id	SWS_FT_FI2
Number of Residues	28
Details	BINDING:

Chain	Residue	Details
A	ASN37
B	GLU262
B	ARG283
B	HIS312
B	ASP316
B	GLU339
C	ASN37
C	HIS122
C	GLU262
C	ARG283
C	HIS312
A	HIS122
C	ASP316
C	GLU339
D	ASN37
D	HIS122
D	GLU262
D	ARG283
D	HIS312
D	ASP316
D	GLU339
A	GLU262
A	ARG283
A	HIS312
A	ASP316
A	GLU339
B	ASN37
B	HIS122

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:17944491

Chain	Residue	Details
A	ASP210
A	GLU236
B	ASP210
B	GLU236
C	ASP210
C	GLU236
D	ASP210
D	GLU236

site_id	SWS_FT_FI4
Number of Residues	4
Details	SITE: Important for activity and substrate specificity; Ala is observed in family members with high D-mannonate dehydratase activity that have no activity with D-gluconate

Chain	Residue	Details
A	PRO314
B	PRO314
C	PRO314
D	PRO314

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	9
Details	M-CSA 960

Chain	Residue	Details
A	ARG147	modifies pKa
A	TYR159	proton acceptor, proton donor
A	ASP210	metal ligand
A	HIS212	proton acceptor, proton donor
A	GLU236	metal ligand
A	GLU262	metal ligand
A	ARG283	electrostatic stabiliser
A	GLU339	electrostatic stabiliser
A	TRP402	modifies pKa

site_id	MCSA2
Number of Residues	9
Details	M-CSA 960

Chain	Residue	Details
B	ARG147	modifies pKa
B	TYR159	proton acceptor, proton donor
B	ASP210	metal ligand
B	HIS212	proton acceptor, proton donor
B	GLU236	metal ligand
B	GLU262	metal ligand
B	ARG283	electrostatic stabiliser
B	GLU339	electrostatic stabiliser
B	TRP402	modifies pKa

site_id	MCSA3
Number of Residues	9
Details	M-CSA 960

Chain	Residue	Details
C	ARG147	modifies pKa
C	TYR159	proton acceptor, proton donor
C	ASP210	metal ligand
C	HIS212	proton acceptor, proton donor
C	GLU236	metal ligand
C	GLU262	metal ligand
C	ARG283	electrostatic stabiliser
C	GLU339	electrostatic stabiliser
C	TRP402	modifies pKa

site_id	MCSA4
Number of Residues	9
Details	M-CSA 960

Chain	Residue	Details
D	ARG147	modifies pKa
D	TYR159	proton acceptor, proton donor
D	ASP210	metal ligand
D	HIS212	proton acceptor, proton donor
D	GLU236	metal ligand
D	GLU262	metal ligand
D	ARG283	electrostatic stabiliser
D	GLU339	electrostatic stabiliser
D	TRP402	modifies pKa

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