2QJN

Crystal structure of D-mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and 2-keto-3-deoxy-D-gluconate

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 1001

Chain	Residue
A	ASP210
A	GLU236
A	GLU262
A	KDG2001
A	HOH2154

---

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 1002

Chain	Residue
B	HOH2173
B	ASP210
B	GLU236
B	GLU262
B	KDG2002

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 1003

Chain	Residue
C	ASP210
C	GLU236
C	GLU262
C	KDG2003
C	HOH2157

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 1004

Chain	Residue
D	ASP210
D	GLU236
D	GLU262
D	KDG2004
D	HOH2139

---

site_id	AC5
Number of Residues	17
Details	BINDING SITE FOR RESIDUE KDG A 2001

Chain	Residue
A	ASN37
A	HIS122
A	ARG147
A	ASP210
A	HIS212
A	GLU236
A	GLU262
A	ARG283
A	HIS312
A	ALA314
A	ASP316
A	GLU339
A	LEU389
A	TRP402
A	MG1001
A	HOH2054
B	TRP76

---

site_id	AC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE KDG B 2002

Chain	Residue
A	TRP76
B	ASN37
B	HIS122
B	ASP210
B	HIS212
B	GLU236
B	GLU262
B	ARG283
B	HIS312
B	ALA314
B	ASP316
B	GLU339
B	LEU389
B	TRP402
B	MG1002
B	HOH2028

---

site_id	AC7
Number of Residues	17
Details	BINDING SITE FOR RESIDUE KDG C 2003

Chain	Residue
C	ASN37
C	HIS122
C	ARG147
C	ASP210
C	HIS212
C	GLU236
C	GLU262
C	ARG283
C	HIS312
C	ALA314
C	ASP316
C	GLU339
C	MET341
C	TRP402
C	MG1003
C	HOH2007
D	TRP76

---

site_id	AC8
Number of Residues	18
Details	BINDING SITE FOR RESIDUE KDG D 2004

Chain	Residue
C	TYR75
C	TRP76
D	ASN37
D	ARG147
D	ASP210
D	HIS212
D	GLU236
D	GLU262
D	ARG283
D	HIS312
D	ALA314
D	ASP316
D	GLU339
D	MET341
D	LEU389
D	TRP402
D	MG1004
D	HOH2013

---

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	GLU262
B	ASP316
B	GLU339
C	ASN37
C	HIS122
C	GLU262
C	ARG283
C	HIS312
C	ASP316
C	GLU339
D	ASN37
D	HIS122
D	GLU262
D	ARG283
D	HIS312
D	ASP316
D	GLU339
A	ASN37
A	HIS122
A	ARG283
A	HIS312
A	ASP316
A	GLU339
B	ASN37
B	HIS122
B	GLU262
B	ARG283
B	HIS312

---

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	ALA314
B	ALA314
C	ALA314
D	ALA314

---

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

---