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Title :   CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION

Authors :   W. Furey, F. Dyda

Date :   23 Mar 93 (Deposition) - 30 Apr 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Lyase(Carbon-Carbon) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Dyda, W. Furey, S. Swaminathan, M. Sax, B. Farrenkopf, F. Jordan
Catalytic Centers In The Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase At 2. 4-A Resolution.
Biochemistry V. 32 6165 1993
PubMed-ID: 8512926 | Reference-DOI: 10.1021/BI00075A008
(for further references see the PDB file header)

Molecule 1 - PYRUVATE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.1
	Engineered	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	TDP	2	Ligand/Ion	THIAMIN DIPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:444 , ASN A:471 , GLY A:473 , TDP A:557 , HOH A:560	BINDING SITE FOR RESIDUE MG A 559
2	AC2	SOFTWARE	ASP B:444 , ASN B:471 , GLY B:473 , TDP B:557 , HOH B:560	BINDING SITE FOR RESIDUE MG B 559
3	AC3	SOFTWARE	THR A:390 , GLY A:413 , ILE A:415 , GLY A:443 , ASP A:444 , GLY A:445 , SER A:446 , ASN A:471 , GLY A:473 , TYR A:474 , THR A:475 , ILE A:476 , GLU A:477 , MG A:559 , HOH A:560 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76	BINDING SITE FOR RESIDUE TDP A 557
4	AC4	SOFTWARE	PRO A:26 , GLY A:27 , GLU A:51 , VAL A:76 , GLY B:389 , THR B:390 , GLY B:413 , ILE B:415 , GLY B:443 , ASP B:444 , GLY B:445 , SER B:446 , ASN B:471 , GLY B:473 , TYR B:474 , THR B:475 , ILE B:476 , GLU B:477 , MG B:559 , HOH B:560	BINDING SITE FOR RESIDUE TDP B 557
5	TD1	UNKNOWN	THR A:388 , THR A:390 , GLY A:413 , ILE A:415 , ASP A:444 , SER A:446 , LEU A:449 , LEU A:469 , ASN A:471 , ILE A:476 , GLY A:473 , GLU A:477 , LEU B:25 , ASP B:28 , GLU B:51 , THR B:73 , VAL B:76 , ASN B:83 , HIS B:114 , HIS B:115	NULL
6	TD2	UNKNOWN	THR B:388 , THR B:390 , GLY B:413 , ILE B:415 , ASP B:444 , SER B:446 , LEU B:449 , LEU B:469 , ASN B:471 , ILE B:476 , GLY B:473 , GLU B:477 , LEU A:25 , ASP A:28 , GLU A:51 , THR A:73 , VAL A:76 , ASN A:83 , HIS A:114 , HIS A:115	NULL

(no "SS Bond" information available for 1PYD)

(no "Cis Peptide Bond" information available for 1PYD)

(no "SAP(SNP)/Variant" information available for 1PYD)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC1_YEAST	427-446	2	A:427-446 B:427-446

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR044C	1	YLR044C.1	XII:234082-232391	1692	PDC1_YEAST	1-563	563	2	A:2-556 (gaps) B:2-556 (gaps)	555 555

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:537
 aligned with PDC1_YEAST | P06169 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:555
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
           PDC1_YEAST     2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVEQAKLT 556
               SCOP domains d1pyda2 A:2-181 Pyruvate decarboxylase                                                                                                                                              d1pyda1 A:182-360 Pyruvate decarboxylase                                                                                                                                           d1pyda3 A:361-556 Pyruvate decarboxylase                                                                                                                                                             SCOP domains
               CATH domains 1pydA01 A:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       1pydA02 A:189-352 TPP-binding domain                                                                                                                                1pydA03 A:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...eeeee......hhhhhhhhh....eee....hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeeeee....--------..........hhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeee.hhhh....hhhhh...........hhhhhhhhhhhhhhhhh...eeeee.hhh.....hhhhhhhhhhh...eee.hhh..........eeee.......hhhhhhhh...eeeee......----------...eeeeee..eeee..eeee...hhhhhhhhhhhhhhh..........................hhhhhhhh........eeeee..hhhhhhhh.......eeee........hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhh....eeeeee....hhhh.......hhh........hhhhh.......eeee..hhhhhhhh...........eeeeee.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         -------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-556 (gaps) UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1pyd A   2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSIS--------HHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSISEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSD----------KTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTNIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVKQAKLT 556
                                    11        21        31        41        51        61        71        81        91       101   |     -  |    121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291         -|      311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
                                                                                                                                 105      114                                                                                                                                                                              291        302

Chain B from PDB  Type:PROTEIN  Length:537
 aligned with PDC1_YEAST | P06169 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:555
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
           PDC1_YEAST     2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVEQAKLT 556
               SCOP domains d1pydb2 B:2-181 Pyruvate decarboxylase                                                                                                                                              d1pydb1 B:182-360 Pyruvate decarboxylase                                                                                                                                           d1pydb3 B:361-556 Pyruvate decarboxylase                                                                                                                                                             SCOP domains
               CATH domains 1pydB01 B:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       1pydB02 B:189-352 TPP-binding domain                                                                                                                                1pydB03 B:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    -- CATH domains
           Pfam domains (1) --TPP_enzyme_N-1pydB05 B:4-180                                                                                                                                                     --------------------TPP_enzyme_M-1pydB01 B:201-339                                                                                                             -----------------------------------------------TPP_enzyme_C-1pydB03 B:387-526                                                                                                              ------------------------------ Pfam domains (1)
           Pfam domains (2) --TPP_enzyme_N-1pydB06 B:4-180                                                                                                                                                     --------------------TPP_enzyme_M-1pydB02 B:201-339                                                                                                             -----------------------------------------------TPP_enzyme_C-1pydB04 B:387-526                                                                                                              ------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhh...eeeee......hhhhhhhhh....eee....hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeeeee....--------..........hhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeee.hhhh....hhhhh...........hhhhhhhhhhhhhhhhh...eeeee.hhh.....hhhhhhhhhhh...eee.hhh..........eeee.......hhhhhhhh...eeeee......----------...eeeeee..eeee..eeee...hhhhhhhhhhhhhhh..........................hhhhhhhh........eeeee..hhhhhhhh.......eeee........hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhh....eeeeee....hhhh.......hhh........hhhhh.......eeee..hhhhhhhh...........eeeeee.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         -------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-556 (gaps) UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1pyd B   2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSIS--------HHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSISEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSD----------KTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTNIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVKQAKLT 556
                                    11        21        31        41        51        61        71        81        91       101   |     -  |    121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291         -|      311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
                                                                                                                                 105      114                                                                                                                                                                              291        302

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.970, no name defined] (144)

Baker's yeast (Saccharomyces cerevisiae) (17)

1a	1pydA03	A:353-554
1b	1pydB03	B:353-554
1c	1pydA01	A:2-188
1d	1pydB01	B:2-188

Homologous Superfamily: TPP-binding domain (120)

Baker's yeast (Saccharomyces cerevisiae) (20)

2a	1pydA02	A:189-352
2b	1pydB02	B:189-352

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDC1_YEAST | P06169)

molecular function
	GO:0047433	branched-chain-2-oxoacid decarboxylase activity	Catalysis of the reaction: (S)-3-methyl-2-oxopentanoate + H(+) = 2-methylbutanal + CO(2).
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0047434	indolepyruvate decarboxylase activity	Catalysis of the reaction: indolepyruvate = CO2 + indole acetaldehyde.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0050177	phenylpyruvate decarboxylase activity	Catalysis of the reaction: phenylpyruvate = phenylacetaldehyde + CO2.
	GO:0004737	pyruvate decarboxylase activity	Catalysis of the reaction: a 2-oxo acid = an aldehyde + CO2.
	GO:0030976	thiamine pyrophosphate binding	Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
biological process
	GO:0006559	L-phenylalanine catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
	GO:0000955	amino acid catabolic process via Ehrlich pathway	The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols.
	GO:0000949	aromatic amino acid family catabolic process to alcohol via Ehrlich pathway	The chemical reactions and pathways involving the catabolism of aromatic amino acids to produce aromatic alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanol, 4-hydroxyphenylethanol, or tryptophol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols.
	GO:0009083	branched-chain amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0019655	glycolytic fermentation to ethanol	The anaerobic chemical reactions and pathways resulting in the breakdown of glucose; it is converted into ethanol and carbon dioxide (CO2), producing two molecules of ATP for each molecule of glucose.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
	GO:0006569	tryptophan catabolic process	The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	PDC1_YEAST \| P06169	:	1pvd 1qpb 2vk1 2vk8 2w93

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Ligands, Modified Residues, Ions (2, 4)

Sites (6, 6)

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