2VJY - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PYRUVATE DECARBOXYLASE FROM KLUYVEROMYCES LACTIS IN COMPLEX WITH THE SUBSTRATE ANALOGUE METHYL ACETYLPHOSPHONATE

Authors :   S. Kutter, G. Wille, M. S. Weiss, S. Konig

Date :   14 Dec 07 (Deposition) - 27 Jan 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Metal-Binding, Decarboxylase, Dimer Of Dimers, Methylacetylphosphonate, Methyl Acetylphosphonate, Substrate Activation, Thiamine Diphosphate, Thiamine Pyrophosphate, Asymmetric Active Sites, Map, Lyase, Pyruvate, Magnesium, Flavoprotein (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
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.1
	Organism Common	:	YEAST
	Organism Scientific	:	KLUYVEROMYCES LACTIS
	Organism Taxid	:	28985

		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 (4, 19)

No.	Name	Count	Type	Full Name
1	ALK	8	Ligand/Ion	(1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^5^-PHOSPHANYL]ETHANOL
2	ALU	3	Ligand/Ion	METHYL HYDROGEN (S)-ACETYLPHOSPHONATE
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	ALK	4	Ligand/Ion	(1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^5^-PHOSPHANYL]ETHANOL
2	ALU	2	Ligand/Ion	METHYL HYDROGEN (S)-ACETYLPHOSPHONATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	ALK	4	Ligand/Ion	(1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^5^-PHOSPHANYL]ETHANOL
2	ALU	1	Ligand/Ion	METHYL HYDROGEN (S)-ACETYLPHOSPHONATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (19, 19)

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 , ALK A:602 , HOH A:2209 , HOH A:2238 , HOH A:2298 , 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:2238	BINDING SITE FOR RESIDUE MG A 601
03	AC3	SOFTWARE	PHE A:292 , THR A:388 , GLU A:477 , ILE A:480 , TPP A:600 , GLY B:27 , ASP B:28 , HIS B:114 , HIS B:115 , HOH B:2042	BINDING SITE FOR RESIDUE ALK 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 , HOH A:2299 , HOH A:2300	BINDING SITE FOR RESIDUE ALK A 603
05	AC5	SOFTWARE	GLN A:16 , VAL A:17 , GLU A:18 , LYS A:65 , TYR A:157	BINDING SITE FOR RESIDUE ALU A 604
06	AC6	SOFTWARE	PRO A:26 , GLY A:27 , GLU A:51 , VAL A:76 , HIS A:115 , 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 , ALK B:602 , HOH B:2212 , HOH B:2214 , HOH B:2300	BINDING SITE FOR RESIDUE TPP B 600
07	AC7	SOFTWARE	ASP B:444 , ASN B:471 , GLY B:473 , TPP B:600 , HOH B:2300	BINDING SITE FOR RESIDUE MG B 601
08	AC8	SOFTWARE	GLY A:27 , ASP A:28 , HIS A:114 , HIS A:115 , HOH A:2014 , PHE B:292 , THR B:388 , GLU B:477 , ILE B:480 , TPP B:600	BINDING SITE FOR RESIDUE ALK B 602
09	AC9	SOFTWARE	HIS B:92 , CYS B:221 , HIS B:225 , GLY B:286 , ALA B:287 , HIS B:310 , SER B:311 , HOH B:2161	BINDING SITE FOR RESIDUE ALK B 603
10	BC1	SOFTWARE	VAL B:17 , LYS B:65 , TYR B:157	BINDING SITE FOR RESIDUE ALU B 604
11	BC2	SOFTWARE	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 , ALK C:602 , HOH C:2164 , HOH C:2219 , HOH C:2220 , PRO D:26 , GLY D:27 , GLU D:51 , VAL D:76 , HIS D:115	BINDING SITE FOR RESIDUE TPP C 600
12	BC3	SOFTWARE	ASP C:444 , ASN C:471 , GLY C:473 , TPP C:600 , HOH C:2220	BINDING SITE FOR RESIDUE MG C 601
13	BC4	SOFTWARE	PHE C:292 , THR C:388 , GLU C:477 , ILE C:480 , TPP C:600 , GLY D:27 , ASP D:28 , HIS D:114 , HIS D:115 , HOH D:2022	BINDING SITE FOR RESIDUE ALK C 602
14	BC5	SOFTWARE	HIS C:92 , CYS C:221 , HIS C:225 , GLY C:286 , ALA C:287 , HIS C:310 , SER C:311 , HOH C:2126	BINDING SITE FOR RESIDUE ALK C 603
15	BC6	SOFTWARE	GLN C:16 , VAL C:17 , GLU C:18 , LYS C:65 , TYR C:157	BINDING SITE FOR RESIDUE ALU C 604
16	BC7	SOFTWARE	PRO C:26 , GLY C:27 , GLU C:51 , VAL C:76 , HIS C:115 , 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 , ALK D:602 , HOH D:2164 , HOH D:2184 , HOH D:2227	BINDING SITE FOR RESIDUE TPP D 600
17	BC8	SOFTWARE	ASP D:444 , ASN D:471 , GLY D:473 , TPP D:600 , HOH D:2184	BINDING SITE FOR RESIDUE MG D 601
18	BC9	SOFTWARE	GLY C:27 , ASP C:28 , HIS C:114 , HIS C:115 , THR D:388 , GLU D:477 , ILE D:480 , TPP D:600	BINDING SITE FOR RESIDUE ALK D 602
19	CC1	SOFTWARE	HIS D:92 , CYS D:221 , HIS D:225 , GLY D:286 , ALA D:287 , HIS D:310 , SER D:311 , HOH D:2228	BINDING SITE FOR RESIDUE ALK D 603

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC1_KLULA	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_KLULA	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_KLULA	427-446	2	- - C:427-446 D:427-446

(no "Exon" information available for 2VJY)

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_KLULA | Q12629 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_KLULA     2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 563
               SCOP domains d2vjya1 A:2-181 automated matches                                                                                                                                                   d2vjya2 A:182-360 automated matches                                                                                                                                                d2vjya3 A:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vjyA01 A:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vjyA02 A:189-352 TPP-binding domain                                                                                                                                2vjyA03 A:353-554  [code=3.40.50.970, no name defined]                                                                                                                                                    --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhh.............hhhhhhhhh....eee.....hhhhhhhhhhhhhhhhh..eeeeee.hhhh.eee.hhhhh.........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhh..eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhh.........eeeeeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjy A   2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 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_KLULA | Q12629 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_KLULA     2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 563
               SCOP domains d2vjyb1 B:2-181 automated matches                                                                                                                                                   d2vjyb2 B:182-360 automated matches                                                                                                                                                d2vjyb3 B:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vjyB01 B:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vjyB02 B:189-352 TPP-binding domain                                                                                                                                2vjyB03 B:353-553  [code=3.40.50.970, no name defined]                                                                                                                                                   ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh.............hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..eeeeee......eee.hhhhh.........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee.hhhh.........eeee.hhhhhhhhhhhhhhh..eeeee.....hhhhh..........eeee...eeee..eeee..hhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhh....eeee..hhhhhhhh........eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhh.........eeeeeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjy B   2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 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_KLULA | Q12629 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_KLULA     2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 563
               SCOP domains d2vjyc1 C:2-181 automated matches                                                                                                                                                   d2vjyc2 C:182-360 automated matches                                                                                                                                                d2vjyc3 C:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vjyC01 C:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vjyC02 C:189-352 TPP-binding domain                                                                                                                                2vjyC03 C:353-553  [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..hhhhhhhhhhhhhhhhhhhh..eeeeee......eee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhh..eeeee.....hhhhh..........eeee...eeee..eeee..hhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhh.........eeeeeee......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjy C   2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 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_KLULA | Q12629 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_KLULA     2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 563
               SCOP domains d2vjyd1 D:2-181 automated matches                                                                                                                                                   d2vjyd2 D:182-360 automated matches                                                                                                                                                d2vjyd3 D:361-563 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 2vjyD01 D:2-188  [code=3.40.50.970, no name defined]                                                                                                                                       2vjyD02 D:189-352 TPP-binding domain                                                                                                                                2vjyD03 D: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.hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh.............hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..eeeeee......eee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhh..eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjy D   2 SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN 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)

Milk yeast (Kluyveromyces lactis) [TaxId: 28985] (2)

1a	d2vjya2	A:182-360
1b	d2vjyb2	B:182-360
1c	d2vjyc2	C:182-360
1d	d2vjyd2	D: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)

Milk yeast (Kluyveromyces lactis) [TaxId: 28985] (2)

2a	d2vjya1	A:2-181
2b	d2vjyb1	B:2-181
2c	d2vjyb3	B:361-563
2d	d2vjyc1	C:2-181
2e	d2vjyc3	C:361-563
2f	d2vjyd1	D:2-181
2g	d2vjyd3	D:361-563
2h	d2vjya3	A: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 (Kluyveromyces lactis) (1)

1a	2vjyA03	A:353-554
1b	2vjyD03	D:353-554
1c	2vjyB03	B:353-553
1d	2vjyC03	C:353-553
1e	2vjyA01	A:2-188
1f	2vjyB01	B:2-188
1g	2vjyC01	C:2-188
1h	2vjyD01	D:2-188

Homologous Superfamily: TPP-binding domain (120)

Yeast (Kluyveromyces lactis) (1)

2a	2vjyA02	A:189-352
2b	2vjyB02	B:189-352
2c	2vjyC02	C:189-352
2d	2vjyD02	D:189-352

(no "Pfam Domain" information available for 2VJY)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDC1_KLULA | Q12629)


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: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: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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vjy)

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	2vjy
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	PDC1_KLULA \| Q12629	:	2vk4

2g1i	CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROMKLUYVEROMYCES LACTIS
2vk4	CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROM KLUYVEROMYCES LACTIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 12)

CATH Domains (2, 12)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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