Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2VK8

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0000949	biological_process	aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
A	0000955	biological_process	amino acid catabolic process via Ehrlich pathway
A	0003824	molecular_function	catalytic activity
A	0004737	molecular_function	pyruvate decarboxylase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006090	biological_process	pyruvate metabolic process
A	0006559	biological_process	L-phenylalanine catabolic process
A	0006569	biological_process	tryptophan catabolic process
A	0009083	biological_process	branched-chain amino acid catabolic process
A	0016831	molecular_function	carboxy-lyase activity
A	0019655	biological_process	glycolytic fermentation to ethanol
A	0030976	molecular_function	thiamine pyrophosphate binding
A	0046872	molecular_function	metal ion binding
A	0047433	molecular_function	branched-chain-2-oxoacid decarboxylase activity
A	0047434	molecular_function	indolepyruvate decarboxylase activity
A	0050177	molecular_function	phenylpyruvate decarboxylase activity
B	0000287	molecular_function	magnesium ion binding
B	0000949	biological_process	aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
B	0000955	biological_process	amino acid catabolic process via Ehrlich pathway
B	0003824	molecular_function	catalytic activity
B	0004737	molecular_function	pyruvate decarboxylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006090	biological_process	pyruvate metabolic process
B	0006559	biological_process	L-phenylalanine catabolic process
B	0006569	biological_process	tryptophan catabolic process
B	0009083	biological_process	branched-chain amino acid catabolic process
B	0016831	molecular_function	carboxy-lyase activity
B	0019655	biological_process	glycolytic fermentation to ethanol
B	0030976	molecular_function	thiamine pyrophosphate binding
B	0046872	molecular_function	metal ion binding
B	0047433	molecular_function	branched-chain-2-oxoacid decarboxylase activity
B	0047434	molecular_function	indolepyruvate decarboxylase activity
B	0050177	molecular_function	phenylpyruvate decarboxylase activity
C	0000287	molecular_function	magnesium ion binding
C	0000949	biological_process	aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
C	0000955	biological_process	amino acid catabolic process via Ehrlich pathway
C	0003824	molecular_function	catalytic activity
C	0004737	molecular_function	pyruvate decarboxylase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006090	biological_process	pyruvate metabolic process
C	0006559	biological_process	L-phenylalanine catabolic process
C	0006569	biological_process	tryptophan catabolic process
C	0009083	biological_process	branched-chain amino acid catabolic process
C	0016831	molecular_function	carboxy-lyase activity
C	0019655	biological_process	glycolytic fermentation to ethanol
C	0030976	molecular_function	thiamine pyrophosphate binding
C	0046872	molecular_function	metal ion binding
C	0047433	molecular_function	branched-chain-2-oxoacid decarboxylase activity
C	0047434	molecular_function	indolepyruvate decarboxylase activity
C	0050177	molecular_function	phenylpyruvate decarboxylase activity
D	0000287	molecular_function	magnesium ion binding
D	0000949	biological_process	aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
D	0000955	biological_process	amino acid catabolic process via Ehrlich pathway
D	0003824	molecular_function	catalytic activity
D	0004737	molecular_function	pyruvate decarboxylase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006090	biological_process	pyruvate metabolic process
D	0006559	biological_process	L-phenylalanine catabolic process
D	0006569	biological_process	tryptophan catabolic process
D	0009083	biological_process	branched-chain amino acid catabolic process
D	0016831	molecular_function	carboxy-lyase activity
D	0019655	biological_process	glycolytic fermentation to ethanol
D	0030976	molecular_function	thiamine pyrophosphate binding
D	0046872	molecular_function	metal ion binding
D	0047433	molecular_function	branched-chain-2-oxoacid decarboxylase activity
D	0047434	molecular_function	indolepyruvate decarboxylase activity
D	0050177	molecular_function	phenylpyruvate decarboxylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	25
Details	BINDING SITE FOR RESIDUE TPP A 1564

Chain	Residue
A	GLY389
A	ASN471
A	GLY473
A	TYR474
A	THR475
A	ILE476
A	GLN477
A	MG1565
A	HOH2295
A	HOH2421
A	HOH2422
A	THR390
A	HOH2423
B	PRO26
B	GLY27
B	GLU51
B	VAL76
B	HIS115
A	GLY413
A	SER414
A	ILE415
A	GLY443
A	ASP444
A	GLY445
A	SER446

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 1565

Chain	Residue
A	ASP444
A	ASN471
A	GLY473
A	TPP1564
A	HOH2421

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 2OP A 1566

Chain	Residue
A	HIS92
A	CYS221
A	GLY286
A	ALA287
A	HIS310
A	SER311

site_id	AC4
Number of Residues	25
Details	BINDING SITE FOR RESIDUE TPP B 1564

Chain	Residue
A	PRO26
A	GLY27
A	GLU51
A	VAL76
A	HIS115
B	GLY389
B	THR390
B	GLY413
B	SER414
B	ILE415
B	GLY443
B	ASP444
B	GLY445
B	SER446
B	ASN471
B	GLY473
B	TYR474
B	THR475
B	ILE476
B	GLN477
B	MG1565
B	HOH2375
B	HOH2376
B	HOH2421
B	HOH2533

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 1565

Chain	Residue
B	ASP444
B	ASN471
B	GLY473
B	TPP1564
B	HOH2421

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 2OP B 1566

Chain	Residue
B	HIS92
B	CYS221
B	HIS225
B	GLY286
B	ALA287
B	HIS310
B	SER311
B	HOH2288

site_id	AC7
Number of Residues	25
Details	BINDING SITE FOR RESIDUE TPP C 1564

Chain	Residue
C	GLY389
C	THR390
C	GLY413
C	SER414
C	ILE415
C	GLY443
C	ASP444
C	GLY445
C	SER446
C	ASN471
C	GLY473
C	TYR474
C	THR475
C	ILE476
C	GLN477
C	MG1565
C	HOH2289
C	HOH2325
C	HOH2432
C	HOH2433
D	PRO26
D	GLY27
D	GLU51
D	VAL76
D	HIS115

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 1565

Chain	Residue
C	ASP444
C	ASN471
C	GLY473
C	TPP1564
C	HOH2325

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE 2OP C 1566

Chain	Residue
C	CYS221
C	GLY286
C	ALA287
C	HIS310
C	SER311

site_id	BC1
Number of Residues	25
Details	BINDING SITE FOR RESIDUE TPP D 1564

Chain	Residue
C	PRO26
C	GLY27
C	GLU51
C	VAL76
C	HIS115
D	GLY389
D	THR390
D	GLY413
D	SER414
D	ILE415
D	GLY443
D	ASP444
D	GLY445
D	SER446
D	ASN471
D	GLY473
D	TYR474
D	THR475
D	ILE476
D	GLN477
D	MG1565
D	HOH2296
D	HOH2427
D	HOH2428
D	HOH2429

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 1565

Chain	Residue
D	ASP444
D	ASN471
D	GLY473
D	TPP1564
D	HOH2428

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 2OP D 1566

Chain	Residue
D	HIS92
D	CYS221
D	HIS225
D	GLY286
D	ALA287
D	HIS310
D	SER311
D	HOH2225

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	PHE427-SER446

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	BINDING: BINDING => ECO:0000305\|PubMed:10651824

Chain	Residue	Details
A	ASP28
D	ASP28
D	TYR157
D	GLN477
A	TYR157
A	GLN477
B	ASP28
B	TYR157
B	GLN477
C	ASP28
C	TYR157
C	GLN477

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000305\|PubMed:10651824, ECO:0007744\|PDB:1QPB

Chain	Residue	Details
A	HIS115
A	ARG224
B	HIS115
B	ARG224
C	HIS115
C	ARG224
D	HIS115
D	ARG224

site_id	SWS_FT_FI3
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:10651824, ECO:0007744\|PDB:1QPB

Chain	Residue	Details
A	THR390
B	GLY445
B	ASN471
B	GLY473
C	THR390
C	GLY413
C	ASP444
C	GLY445
C	ASN471
C	GLY473
D	THR390
A	GLY413
D	GLY413
D	ASP444
D	GLY445
D	ASN471
D	GLY473
A	ASP444
A	GLY445
A	ASN471
A	GLY473
B	THR390
B	GLY413
B	ASP444

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N-acetylserine => ECO:0000269\|PubMed:10545125, ECO:0000269\|PubMed:9298649

Chain	Residue	Details
A	SER2
B	SER2
C	SER2
D	SER2

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: Omega-N-methylarginine => ECO:0000269\|PubMed:26046779

Chain	Residue	Details
A	ARG161
B	ARG161
C	ARG161
D	ARG161

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17330950, ECO:0007744\|PubMed:18407956, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
A	SER223
B	SER223
C	SER223
D	SER223

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
A	THR266
B	THR266
C	THR266
D	THR266

site_id	SWS_FT_FI8
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
A	THR336
A	THR522
B	THR336
B	THR522
C	THR336
C	THR522
D	THR336
D	THR522

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:17330950, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
A	THR353
B	THR353
C	THR353
D	THR353

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
A	SER526
B	SER526
C	SER526
D	SER526

site_id	SWS_FT_FI11
Number of Residues	32
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744\|PubMed:22106047

Chain	Residue	Details
A	LYS212
B	LYS233
B	LYS269
B	LYS332
B	LYS484
B	LYS505
B	LYS520
C	LYS212
C	LYS233
C	LYS269
C	LYS332
C	LYS484
C	LYS505
C	LYS520
D	LYS212
D	LYS233
D	LYS269
D	LYS332
A	LYS233
D	LYS484
D	LYS505
D	LYS520
A	LYS269
A	LYS332
A	LYS484
A	LYS505
A	LYS520
B	LYS212

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	Annotated By Reference To The Literature 1pvd

Chain	Residue	Details
A	ASP28
A	HIS114
A	HIS115
A	GLN477

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 1pvd

Chain	Residue	Details
B	ASP28
B	HIS114
B	HIS115
B	GLN477

site_id	CSA3
Number of Residues	4
Details	Annotated By Reference To The Literature 1pvd

Chain	Residue	Details
C	ASP28
C	HIS114
C	HIS115
C	GLN477

site_id	CSA4
Number of Residues	4
Details	Annotated By Reference To The Literature 1pvd

Chain	Residue	Details
D	ASP28
D	HIS114
D	HIS115
D	GLN477

site_id	MCSA1
Number of Residues	9
Details	M-CSA 215

Chain	Residue	Details
A	ASP28	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	GLU51	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	HIS114	activator, electrostatic stabiliser, hydrogen bond donor, polar interaction
A	HIS115	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor
A	GLY413	activator, electrostatic stabiliser, hydrogen bond acceptor
A	ASP444	metal ligand
A	ASN471	metal ligand
A	GLY473	metal ligand
A	GLN477	electrostatic stabiliser, polar interaction

site_id	MCSA2
Number of Residues	9
Details	M-CSA 215

Chain	Residue	Details
B	ASP28	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	GLU51	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	HIS114	activator, electrostatic stabiliser, hydrogen bond donor, polar interaction
B	HIS115	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor
B	GLY413	activator, electrostatic stabiliser, hydrogen bond acceptor
B	ASP444	metal ligand
B	ASN471	metal ligand
B	GLY473	metal ligand
B	GLN477	electrostatic stabiliser, polar interaction

site_id	MCSA3
Number of Residues	9
Details	M-CSA 215

Chain	Residue	Details
C	ASP28	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
C	GLU51	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	HIS114	activator, electrostatic stabiliser, hydrogen bond donor, polar interaction
C	HIS115	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor
C	GLY413	activator, electrostatic stabiliser, hydrogen bond acceptor
C	ASP444	metal ligand
C	ASN471	metal ligand
C	GLY473	metal ligand
C	GLN477	electrostatic stabiliser, polar interaction

site_id	MCSA4
Number of Residues	9
Details	M-CSA 215

Chain	Residue	Details
D	ASP28	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
D	GLU51	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	HIS114	activator, electrostatic stabiliser, hydrogen bond donor, polar interaction
D	HIS115	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor
D	GLY413	activator, electrostatic stabiliser, hydrogen bond acceptor
D	ASP444	metal ligand
D	ASN471	metal ligand
D	GLY473	metal ligand
D	GLN477	electrostatic stabiliser, polar interaction

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