2VK1 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT D28A IN COMPLEX WITH ITS SUBSTRATE

Authors :   S. Kutter, M. Weik, M. S. Weiss, S. Konig

Date :   16 Dec 07 (Deposition) - 27 Jan 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.71

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Asymmetric Active Sites, Phenylalanine Catabolism, Tryptophan Catabolism, Thiamine Pyrophosphate, Dimer Of Dimers, Phosphorylation, Allosteric Enzyme, Tdp, Tpp, Lyase, Nucleus, Pyruvate, Cytoplasm, Branched-Chain Amino Acid Catabolism, Substrate Activation, Thiamine Diphosphate, Magnesium, Acetylation, Metal-Binding, Decarboxylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kutter, M. S. Weiss, G. Wille, R. Golbik, M. Spinka, S. Konig
Covalently Bound Substrate At The Regulatory Site Of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
J. Biol. Chem. V. 284 12136 2009
PubMed-ID: 19246454 | Reference-DOI: 10.1074/JBC.M806228200

Molecule 1 - PYRUVATE DECARBOXYLASE ISOZYME 1
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC 18
	Expression System Strain	:	JM 109
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PYRUVATE DECARBOXYLASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	PYR	8	Ligand/Ion	PYRUVIC ACID
3	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PYR	4	Ligand/Ion	PYRUVIC ACID
3	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PYR	4	Ligand/Ion	PYRUVIC ACID
3	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:389 , THR A:390 , GLY A:413 , SER A:414 , 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:601 , PYR A:602 , HOH A:2314 , HOH A:2434 , HOH A:2435 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76 , HIS B:115	BINDING SITE FOR RESIDUE TPP A 600
02	AC2	SOFTWARE	ASP A:444 , ASN A:471 , GLY A:473 , TPP A:600 , HOH A:2435	BINDING SITE FOR RESIDUE MG A 601
03	AC3	SOFTWARE	GLU A:477 , TPP A:600 , HOH A:2436 , GLY B:27 , ALA B:28 , HIS B:114 , HIS B:115	BINDING SITE FOR RESIDUE PYR A 602
04	AC4	SOFTWARE	HIS A:92 , CYS A:221 , HIS A:225 , GLY A:286 , ALA A:287 , HIS A:310 , SER A:311	BINDING SITE FOR RESIDUE PYR A 603
05	AC5	SOFTWARE	PRO A:26 , GLY A:27 , GLU A:51 , VAL A:76 , HIS A:115 , GLY B:389 , THR B:390 , GLY B:413 , SER B:414 , 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:601 , PYR B:602 , HOH B:2268 , HOH B:2269 , HOH B:2306	BINDING SITE FOR RESIDUE TPP B 600
06	AC6	SOFTWARE	ASP B:444 , ASN B:471 , GLY B:473 , TPP B:600 , HOH B:2306	BINDING SITE FOR RESIDUE MG B 601
07	AC7	SOFTWARE	ALA A:28 , HIS A:114 , HIS A:115 , GLU B:477 , TPP B:600	BINDING SITE FOR RESIDUE PYR B 602
08	AC8	SOFTWARE	HIS B:92 , CYS B:221 , GLY B:286 , ALA B:287 , HIS B:310 , SER B:311 , HOH B:2219	BINDING SITE FOR RESIDUE PYR B 603
09	AC9	SOFTWARE	GLY C:389 , THR C:390 , GLY C:413 , SER C:414 , ILE C:415 , GLY C:443 , ASP C:444 , GLY C:445 , SER C:446 , ASN C:471 , GLY C:473 , TYR C:474 , THR C:475 , ILE C:476 , GLU C:477 , MG C:601 , PYR C:602 , HOH C:2287 , HOH C:2407 , HOH C:2408 , PRO D:26 , GLY D:27 , GLU D:51 , VAL D:76 , HIS D:115	BINDING SITE FOR RESIDUE TPP C 600
10	BC1	SOFTWARE	ASP C:444 , ASN C:471 , GLY C:473 , TPP C:600 , HOH C:2407	BINDING SITE FOR RESIDUE MG C 601
11	BC2	SOFTWARE	GLU C:477 , TPP C:600 , GLY D:27 , ALA D:28 , HIS D:114 , HIS D:115	BINDING SITE FOR RESIDUE PYR C 602
12	BC3	SOFTWARE	HIS C:92 , CYS C:221 , HIS C:225 , GLY C:286 , ALA C:287 , HIS C:310 , SER C:311 , HOH C:2218	BINDING SITE FOR RESIDUE PYR C 603
13	BC4	SOFTWARE	PRO C:26 , GLY C:27 , GLU C:51 , VAL C:76 , HIS C:115 , GLY D:389 , THR D:390 , GLY D:413 , SER D:414 , ILE D:415 , GLY D:443 , ASP D:444 , GLY D:445 , SER D:446 , ASN D:471 , GLY D:473 , TYR D:474 , THR D:475 , ILE D:476 , GLU D:477 , MG D:601 , PYR D:602 , HOH D:2335 , HOH D:2336 , HOH D:2337	BINDING SITE FOR RESIDUE TPP D 600
14	BC5	SOFTWARE	ASP D:444 , ASN D:471 , GLY D:473 , TPP D:600 , HOH D:2336	BINDING SITE FOR RESIDUE MG D 601
15	BC6	SOFTWARE	GLY C:27 , ALA C:28 , HIS C:114 , HIS C:115 , GLU D:477 , TPP D:600	BINDING SITE FOR RESIDUE PYR D 602
16	BC7	SOFTWARE	HIS D:92 , CYS D:221 , GLY D:286 , ALA D:287 , HIS D:310 , SER D:311	BINDING SITE FOR RESIDUE PYR D 603

(no "SS Bond" information available for 2VK1)

(no "Cis Peptide Bond" information available for 2VK1)

(no "SAP(SNP)/Variant" information available for 2VK1)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC1_YEAST	427-446	4	A:427-446 B:427-446 C:427-446 D:427-446

Biological Unit 1 (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 - -

Biological Unit 2 (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	- - C:427-446 D:427-446

Asymmetric Unit (1, 4)

	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	4	A:2-563 B:2-563 C:2-563 D:2-563	562 562 562 562

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:562
 aligned with PDC1_YEAST | P06169 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:562
                                    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       561  
           PDC1_YEAST     2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVEQAKLTAATNAKQ 563
               SCOP domains d2vk1a1 A:2-181 automated matches                                                                                                                                                   d2vk1a2 A:182-360 automated matches                                                                                                                                                d2vk1a3 A:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vk1A01 A:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vk1A02 A:189-352 TPP-binding domain                                                                                                                                2vk1A03 A:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhh.............hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..eeeeee.hhhh.eee.hhhhh.........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhh..eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhhhhhh........................hhhhhhhhhh.......eeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhh.........eeeeeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-563 UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 2vk1 A   2 SEITLGKYLFERLKQVNVNTVFGLPGAFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTAIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVEQAKLTAATNAKQ 563
                                    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       561

Chain B from PDB  Type:PROTEIN  Length:562
 aligned with PDC1_YEAST | P06169 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:562
                                    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       561  
           PDC1_YEAST     2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVEQAKLTAATNAKQ 563
               SCOP domains d2vk1b1 B:2-181 automated matches                                                                                                                                                   d2vk1b2 B:182-360 automated matches                                                                                                                                                d2vk1b3 B:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vk1B01 B:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vk1B02 B:189-352 TPP-binding domain                                                                                                                                2vk1B03 B:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhh.............hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..eeeeee.hhhh.eee.hhhhh.........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhh..eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhhhhhh........................hhhhhhhhhh.......eeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhhh........eeeeeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-563 UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 2vk1 B   2 SEITLGKYLFERLKQVNVNTVFGLPGAFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTAIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVEQAKLTAATNAKQ 563
                                    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       561

Chain C from PDB  Type:PROTEIN  Length:562
 aligned with PDC1_YEAST | P06169 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:562
                                    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       561  
           PDC1_YEAST     2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVEQAKLTAATNAKQ 563
               SCOP domains d2vk1c1 C:2-181 automated matches                                                                                                                                                   d2vk1c2 C:182-360 automated matches                                                                                                                                                d2vk1c3 C:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vk1C01 C:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vk1C02 C:189-352 TPP-binding domain                                                                                                                                2vk1C03 C:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhh.............hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..eeeeee.hhhh.eee.hhhhh.........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhh..eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhhhhhh........................hhhhhhhhhh.......eeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhhh........eeeeeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:2-563 UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 2vk1 C   2 SEITLGKYLFERLKQVNVNTVFGLPGAFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTAIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVEQAKLTAATNAKQ 563
                                    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       561

Chain D from PDB  Type:PROTEIN  Length:562
 aligned with PDC1_YEAST | P06169 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:562
                                    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       561  
           PDC1_YEAST     2 SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVEQAKLTAATNAKQ 563
               SCOP domains d2vk1d1 D:2-181 automated matches                                                                                                                                                   d2vk1d2 D:182-360 automated matches                                                                                                                                                d2vk1d3 D:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vk1D01 D:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vk1D02 D:189-352 TPP-binding domain                                                                                                                                2vk1D03 D:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    --------- CATH domains
           Pfam domains (1) --TPP_enzyme_N-2vk1D09 D:4-180                                                                                                                                                     --------------------TPP_enzyme_M-2vk1D01 D:201-339                                                                                                             -----------------------------------------------TPP_enzyme_C-2vk1D05 D:387-526                                                                                                              ------------------------------------- Pfam domains (1)
           Pfam domains (2) --TPP_enzyme_N-2vk1D10 D:4-180                                                                                                                                                     --------------------TPP_enzyme_M-2vk1D02 D:201-339                                                                                                             -----------------------------------------------TPP_enzyme_C-2vk1D06 D:387-526                                                                                                              ------------------------------------- Pfam domains (2)
           Pfam domains (3) --TPP_enzyme_N-2vk1D11 D:4-180                                                                                                                                                     --------------------TPP_enzyme_M-2vk1D03 D:201-339                                                                                                             -----------------------------------------------TPP_enzyme_C-2vk1D07 D:387-526                                                                                                              ------------------------------------- Pfam domains (3)
           Pfam domains (4) --TPP_enzyme_N-2vk1D12 D:4-180                                                                                                                                                     --------------------TPP_enzyme_M-2vk1D04 D:201-339                                                                                                             -----------------------------------------------TPP_enzyme_C-2vk1D08 D:387-526                                                                                                              ------------------------------------- Pfam domains (4)
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                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:2-563 UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 2vk1 D   2 SEITLGKYLFERLKQVNVNTVFGLPGAFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTAIADAAKGYKPVAVPARTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVEQAKLTAATNAKQ 563
                                    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       561

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: DHS-like NAD/FAD-binding domain (176)

Superfamily: DHS-like NAD/FAD-binding domain (176)

Family: automated matches (36)

Protein domain: automated matches (36)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d2vk1a2	A:182-360
1b	d2vk1c2	C:182-360
1c	d2vk1d2	D:182-360
1d	d2vk1b2	B:182-360

Fold: Thiamin diphosphate-binding fold (THDP-binding) (289)

Superfamily: Thiamin diphosphate-binding fold (THDP-binding) (289)

Family: automated matches (65)

Protein domain: automated matches (65)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

2a	d2vk1a1	A:2-181
2b	d2vk1a3	A:361-563
2c	d2vk1b1	B:2-181
2d	d2vk1b3	B:361-563
2e	d2vk1c1	C:2-181
2f	d2vk1c3	C:361-563
2g	d2vk1d1	D:2-181
2h	d2vk1d3	D:361-563

Asymmetric 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)

Yeast (Saccharomyces cerevisiae) (1)

1a	2vk1A03	A:353-554
1b	2vk1B03	B:353-554
1c	2vk1C03	C:353-554
1d	2vk1D03	D:353-554
1e	2vk1A01	A:2-188
1f	2vk1B01	B:2-188
1g	2vk1C01	C:2-188
1h	2vk1D01	D:2-188

Homologous Superfamily: TPP-binding domain (120)

Yeast (Saccharomyces cerevisiae) (1)

2a	2vk1A02	A:189-352
2b	2vk1B02	B:189-352
2c	2vk1C02	C:189-352
2d	2vk1D02	D:189-352

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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	2vk1
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	4.1.1.1
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	PDC1_YEAST \| P06169	:	1pvd 1pyd 1qpb 2vk8 2w93

1pvd	PYRUVATE DECARBOXYLASE (PDC)
1pyd	PYRUVATE DECARBOXYLASE (PDC)
1qpb	PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (1, 4)

Sequences/Alignments

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SCOP Domains (2, 12)

CATH Domains (2, 12)

Pfam Domains (3, 12)

Gene Ontology (21, 21)

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