Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2V3W

Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003824	molecular_function	catalytic activity
A	0003984	molecular_function	acetolactate synthase activity
A	0016829	molecular_function	lyase activity
A	0016831	molecular_function	carboxy-lyase activity
A	0018924	biological_process	mandelate metabolic process
A	0019596	biological_process	mandelate catabolic process
A	0019752	biological_process	carboxylic acid metabolic process
A	0030976	molecular_function	thiamine pyrophosphate binding
A	0046872	molecular_function	metal ion binding
A	0050660	molecular_function	flavin adenine dinucleotide binding
A	0050695	molecular_function	benzoylformate decarboxylase activity
B	0000287	molecular_function	magnesium ion binding
B	0003824	molecular_function	catalytic activity
B	0003984	molecular_function	acetolactate synthase activity
B	0016829	molecular_function	lyase activity
B	0016831	molecular_function	carboxy-lyase activity
B	0018924	biological_process	mandelate metabolic process
B	0019596	biological_process	mandelate catabolic process
B	0019752	biological_process	carboxylic acid metabolic process
B	0030976	molecular_function	thiamine pyrophosphate binding
B	0046872	molecular_function	metal ion binding
B	0050660	molecular_function	flavin adenine dinucleotide binding
B	0050695	molecular_function	benzoylformate decarboxylase activity
C	0000287	molecular_function	magnesium ion binding
C	0003824	molecular_function	catalytic activity
C	0003984	molecular_function	acetolactate synthase activity
C	0016829	molecular_function	lyase activity
C	0016831	molecular_function	carboxy-lyase activity
C	0018924	biological_process	mandelate metabolic process
C	0019596	biological_process	mandelate catabolic process
C	0019752	biological_process	carboxylic acid metabolic process
C	0030976	molecular_function	thiamine pyrophosphate binding
C	0046872	molecular_function	metal ion binding
C	0050660	molecular_function	flavin adenine dinucleotide binding
C	0050695	molecular_function	benzoylformate decarboxylase activity
D	0000287	molecular_function	magnesium ion binding
D	0003824	molecular_function	catalytic activity
D	0003984	molecular_function	acetolactate synthase activity
D	0016829	molecular_function	lyase activity
D	0016831	molecular_function	carboxy-lyase activity
D	0018924	biological_process	mandelate metabolic process
D	0019596	biological_process	mandelate catabolic process
D	0019752	biological_process	carboxylic acid metabolic process
D	0030976	molecular_function	thiamine pyrophosphate binding
D	0046872	molecular_function	metal ion binding
D	0050660	molecular_function	flavin adenine dinucleotide binding
D	0050695	molecular_function	benzoylformate decarboxylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 1528

Chain	Residue
A	ASP428
A	ASN455
A	THR457
A	TPP1531
A	HOH2226

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 1529

Chain	Residue
C	LEU118
C	ARG120
A	ASN117
A	LEU118
A	ARG120
C	ASN117

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 1528

Chain	Residue
B	ASP428
B	ASN455
B	THR457
B	TPP1531
B	HOH2214

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 1529

Chain	Residue
B	ASN117
B	LEU118
B	ARG120
D	ASN117
D	LEU118
D	ARG120

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 1528

Chain	Residue
C	ASP428
C	ASN455
C	THR457
C	TPP1530
C	HOH2206

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 1528

Chain	Residue
D	ASP428
D	ASN455
D	THR457
D	TPP1530
D	HOH2192

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 1529

Chain	Residue
A	HIS281
A	PHE464
A	TPP1531
C	GLY25
C	SER26
C	HIS70
C	LEU110
C	HOH2246

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 1529

Chain	Residue
B	HIS281
B	TPP1531
D	GLY25
D	SER26
D	HIS70
D	LEU110

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 1530

Chain	Residue
A	GLY25
A	SER26
A	HIS70
A	LEU110
C	HIS281
C	PHE464
C	TPP1530

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 1530

Chain	Residue
B	GLY25
B	SER26
B	HIS70
B	LEU110
B	HOH2240
D	HIS281
D	TPP1530

site_id	BC2
Number of Residues	23
Details	BINDING SITE FOR RESIDUE TPP A 1531

Chain	Residue
A	THR377
A	SER378
A	GLY401
A	LEU403
A	GLY427
A	ASP428
A	GLY429
A	SER430
A	TYR433
A	ASN455
A	THR457
A	TYR458
A	GLY459
A	ALA460
A	MG1528
A	HOH2190
A	HOH2226
C	ASN23
C	PRO24
C	GLU47
C	HIS70
C	ASN77
C	SO41529

site_id	BC3
Number of Residues	24
Details	BINDING SITE FOR RESIDUE TPP B 1531

Chain	Residue
B	HOH2214
D	ASN23
D	PRO24
D	GLY25
D	GLU47
D	HIS70
D	ASN77
D	SO41529
B	THR377
B	SER378
B	GLY401
B	LEU403
B	GLY427
B	ASP428
B	GLY429
B	SER430
B	TYR433
B	ASN455
B	THR457
B	TYR458
B	GLY459
B	ALA460
B	MG1528
B	HOH2176

site_id	BC4
Number of Residues	24
Details	BINDING SITE FOR RESIDUE TPP C 1530

Chain	Residue
A	ASN23
A	PRO24
A	GLY25
A	GLU47
A	HIS70
A	ASN77
A	SO41530
C	THR377
C	SER378
C	GLY401
C	LEU403
C	GLY427
C	ASP428
C	GLY429
C	SER430
C	TYR433
C	ASN455
C	THR457
C	TYR458
C	GLY459
C	ALA460
C	MG1528
C	HOH2206
C	HOH2247

site_id	BC5
Number of Residues	23
Details	BINDING SITE FOR RESIDUE TPP D 1530

Chain	Residue
B	ASN23
B	PRO24
B	GLU47
B	HIS70
B	ASN77
B	SO41530
D	THR377
D	SER378
D	GLY401
D	LEU403
D	GLY427
D	ASP428
D	GLY429
D	SER430
D	TYR433
D	ASN455
D	THR457
D	TYR458
D	GLY459
D	ALA460
D	MG1528
D	HOH2158
D	HOH2192

Functional Information from PROSITE/UniProt

site_id	PS00187
Number of Residues	20
Details	TPP_ENZYMES Thiamine pyrophosphate enzymes signature. IGvqlaePerqvIaViGDGS

Chain	Residue	Details
A	ILE411-SER430

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	332
Details	Region: {"description":"Thiamine pyrophosphate binding"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1bfd

Chain	Residue	Details
A	GLU28
A	HIS281
A	HIS70

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1bfd

Chain	Residue	Details
B	GLU28
B	HIS281
B	HIS70

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1bfd

Chain	Residue	Details
C	GLU28
C	HIS281
C	HIS70

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1bfd

Chain	Residue	Details
D	GLU28
D	HIS281
D	HIS70

site_id	MCSA1
Number of Residues	7
Details	M-CSA 220

Chain	Residue	Details
A	GLY25	electrostatic stabiliser, hydrogen bond donor
A	SER26	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
A	GLU28	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	GLU47	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	HIS70	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	HIS281	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	GLY401	electrostatic stabiliser, hydrogen bond acceptor

site_id	MCSA2
Number of Residues	7
Details	M-CSA 220

Chain	Residue	Details
B	GLY25	electrostatic stabiliser, hydrogen bond donor
B	SER26	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
B	GLU28	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	GLU47	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	HIS70	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	HIS281	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	GLY401	electrostatic stabiliser, hydrogen bond acceptor

site_id	MCSA3
Number of Residues	7
Details	M-CSA 220

Chain	Residue	Details
C	GLY25	electrostatic stabiliser, hydrogen bond donor
C	SER26	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
C	GLU28	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	GLU47	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	HIS70	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
C	HIS281	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	GLY401	electrostatic stabiliser, hydrogen bond acceptor

site_id	MCSA4
Number of Residues	7
Details	M-CSA 220

Chain	Residue	Details
D	GLY25	electrostatic stabiliser, hydrogen bond donor
D	SER26	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
D	GLU28	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	GLU47	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	HIS70	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
D	HIS281	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	GLY401	electrostatic stabiliser, hydrogen bond acceptor

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