Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2W93

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide

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	0006067	biological_process	ethanol metabolic process
A	0006559	biological_process	L-phenylalanine catabolic process
A	0006569	biological_process	L-tryptophan catabolic process
A	0009083	biological_process	branched-chain amino acid catabolic process
A	0016829	molecular_function	lyase activity
A	0016831	molecular_function	carboxy-lyase activity
A	0019655	biological_process	pyruvate 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	0006067	biological_process	ethanol metabolic process
B	0006559	biological_process	L-phenylalanine catabolic process
B	0006569	biological_process	L-tryptophan catabolic process
B	0009083	biological_process	branched-chain amino acid catabolic process
B	0016829	molecular_function	lyase activity
B	0016831	molecular_function	carboxy-lyase activity
B	0019655	biological_process	pyruvate 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	0006067	biological_process	ethanol metabolic process
C	0006559	biological_process	L-phenylalanine catabolic process
C	0006569	biological_process	L-tryptophan catabolic process
C	0009083	biological_process	branched-chain amino acid catabolic process
C	0016829	molecular_function	lyase activity
C	0016831	molecular_function	carboxy-lyase activity
C	0019655	biological_process	pyruvate 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	0006067	biological_process	ethanol metabolic process
D	0006559	biological_process	L-phenylalanine catabolic process
D	0006569	biological_process	L-tryptophan catabolic process
D	0009083	biological_process	branched-chain amino acid catabolic process
D	0016829	molecular_function	lyase activity
D	0016831	molecular_function	carboxy-lyase activity
D	0019655	biological_process	pyruvate 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	22
Details	BINDING SITE FOR RESIDUE TPP A 600

Chain	Residue
A	THR390
A	GLY473
A	TYR474
A	THR475
A	ILE476
A	GLN477
A	MG601
A	HOH2224
A	HOH2351
A	HOH2352
B	PRO26
A	GLY413
B	GLY27
B	GLU51
B	VAL76
A	SER414
A	ILE415
A	GLY443
A	ASP444
A	GLY445
A	SER446
A	ASN471

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 601

Chain	Residue
A	ASP444
A	ASN471
A	GLY473
A	TPP600
A	HOH2351

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PY0 A 603

Chain	Residue
A	CYS221
A	HIS225
A	GLY286
A	ALA287
A	HIS310
A	SER311

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PY0 A 604

Chain	Residue
A	GLN16
A	HOH2353

site_id	AC5
Number of Residues	24
Details	BINDING SITE FOR RESIDUE TPP B 600

Chain	Residue
A	PRO26
A	GLY27
A	GLU51
A	VAL76
A	HIS115
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	MG601
B	PY0602
B	HOH2313
B	HOH2408
B	HOH2409

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 601

Chain	Residue
B	ASP444
B	ASN471
B	GLY473
B	TPP600
B	HOH2313

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PY0 B 602

Chain	Residue
A	ASP28
A	HIS115
B	THR388
B	GLN477
B	ILE480
B	TPP600

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PY0 B 603

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

site_id	AC9
Number of Residues	24
Details	BINDING SITE FOR RESIDUE TPP C 600

Chain	Residue
D	VAL76
D	HIS115
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	MG601
C	PY0602
C	HOH2249
C	HOH2352
C	HOH2353
D	PRO26
D	GLY27
D	GLU51

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 601

Chain	Residue
C	ASP444
C	ASN471
C	GLY473
C	TPP600
C	HOH2353

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PY0 C 602

Chain	Residue
C	THR388
C	GLN477
C	TPP600
D	GLY27
D	ASP28
D	HIS114
D	HIS115

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PY0 C 603

Chain	Residue
C	HIS92
C	CYS221
C	HIS225
C	GLY286
C	ALA287
C	HIS310
C	SER311

site_id	BC4
Number of Residues	24
Details	BINDING SITE FOR RESIDUE TPP D 600

Chain	Residue
C	PRO26
C	GLY27
C	GLU51
C	VAL76
C	HIS115
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	MG601
D	PY0602
D	HOH2295
D	HOH2296
D	HOH2297

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 601

Chain	Residue
D	ASP444
D	ASN471
D	GLY473
D	TPP600
D	HOH2296

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PY0 D 602

Chain	Residue
C	GLY27
C	ASP28
C	HIS115
C	HOH2069
D	THR388
D	GLN477
D	ILE480
D	TPP600

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PY0 D 603

Chain	Residue
D	HIS92
D	CYS221
D	HIS225
D	GLY286
D	ALA287
D	HIS310
D	SER311
D	HOH2298

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 site: {"evidences":[{"source":"PubMed","id":"10651824","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10651824","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1QPB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	48
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10651824","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1QPB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"10545125","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9298649","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"26046779","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	8
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	32
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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)