2WVG - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   STRUCTURAL INSIGHTS INTO THE PRE-REACTION STATE OF PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS

Authors :   X. Y. Pei, K. Erixon, B. F. Luisi, F. J. Leeper

Date :   16 Oct 09 (Deposition) - 09 Feb 10 (Release) - 19 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A,B,E,F
Biol. Unit 1: A,B,E,F  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: A,F  (1x)
Biol. Unit 5: B,E  (1x)

Keywords :   Thiamine Diphosphate, Lyase, Flavoprotein, Metal-Binding, Alcohol Fermentation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Y. Pei, K. Erixon, B. F. Luisi, F. J. Leeper
Structural Insights Into The Pre-Reaction State Of Pyruvate Decarboxylase From Zymomonas Mobilis
Biochemistry V. 49 1727 2010
PubMed-ID: 20099870 | Reference-DOI: 10.1021/BI901864J

Molecule 1 - PYRUVATE DECARBOXYLASE
	Chains	:	A, B, E, F
	EC Number	:	4.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPL450
	Expression System Strain	:	DH5[ALPHA]
	Expression System Taxid	:	668369
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ZYMOMONAS MOBILIS
	Organism Taxid	:	542
	Synonym	:	PDC

		1	2	3	4
Asymmetric Unit	:	A	B	E	F
Biological Unit 1 (1x)	:	A	B	E	F
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			E	F
Biological Unit 4 (1x)	:	A			F
Biological Unit 5 (1x)	:		B	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	F	4	Ligand/Ion	FLUORIDE ION
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	TPU	4	Ligand/Ion	2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	F	-1	Ligand/Ion	FLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TPU	4	Ligand/Ion	2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	F	-1	Ligand/Ion	FLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TPU	2	Ligand/Ion	2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	F	-1	Ligand/Ion	FLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TPU	2	Ligand/Ion	2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	F	-1	Ligand/Ion	FLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TPU	2	Ligand/Ion	2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	F	-1	Ligand/Ion	FLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TPU	2	Ligand/Ion	2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:26 , ASP A:27 , THR A:72 , HIS A:114	BINDING SITE FOR RESIDUE F A 569
02	AC2	SOFTWARE	GLY A:389 , ASP A:390 , GLY A:413 , HIS A:414 , ILE A:415 , GLY A:439 , ASP A:440 , GLY A:441 , SER A:442 , ASN A:467 , GLY A:469 , TYR A:470 , THR A:471 , ILE A:472 , GLU A:473 , MG A:601 , HOH A:2443 , HOH A:2489 , HOH A:2572 , ALA B:25 , GLY B:26 , GLU B:50 , VAL B:75 , HIS B:114	BINDING SITE FOR RESIDUE TPU A 600
03	AC3	SOFTWARE	ASP A:440 , ASN A:467 , GLY A:469 , TPU A:600 , HOH A:2489	BINDING SITE FOR RESIDUE MG A 601
04	AC4	SOFTWARE	GLY B:26 , ASP B:27 , THR B:72 , HIS B:114	BINDING SITE FOR RESIDUE F B 569
05	AC5	SOFTWARE	ALA A:25 , GLY A:26 , GLU A:50 , VAL A:75 , HIS A:114 , GLY B:389 , ASP B:390 , GLY B:413 , HIS B:414 , ILE B:415 , GLY B:439 , ASP B:440 , GLY B:441 , SER B:442 , ASN B:467 , GLY B:469 , TYR B:470 , THR B:471 , ILE B:472 , GLU B:473 , MG B:601 , HOH B:2409 , HOH B:2454 , HOH B:2548 , HOH B:2549	BINDING SITE FOR RESIDUE TPU B 600
06	AC6	SOFTWARE	ASP B:440 , ASN B:467 , GLY B:469 , TPU B:600 , HOH B:2448	BINDING SITE FOR RESIDUE MG B 601
07	AC7	SOFTWARE	GLY E:26 , ASP E:27 , THR E:72 , HIS E:114	BINDING SITE FOR RESIDUE F E 569
08	AC8	SOFTWARE	GLY E:389 , ASP E:390 , GLY E:413 , HIS E:414 , ILE E:415 , GLY E:439 , ASP E:440 , GLY E:441 , SER E:442 , ASN E:467 , GLY E:469 , TYR E:470 , THR E:471 , ILE E:472 , GLU E:473 , MG E:601 , HOH E:2478 , HOH E:2481 , HOH E:2628 , HOH E:2629 , ALA F:25 , GLY F:26 , GLU F:50 , VAL F:75 , HIS F:114	BINDING SITE FOR RESIDUE TPU E 600
09	AC9	SOFTWARE	ASP E:440 , ASN E:467 , GLY E:469 , TPU E:600 , HOH E:2528	BINDING SITE FOR RESIDUE MG E 601
10	BC1	SOFTWARE	ASP F:440 , ASN F:467 , GLY F:469 , TPU F:600 , HOH F:2497	BINDING SITE FOR RESIDUE MG F 569
11	BC2	SOFTWARE	GLY F:26 , ASP F:27 , THR F:72 , HIS F:114	BINDING SITE FOR RESIDUE F F 570
12	BC3	SOFTWARE	ALA E:25 , GLY E:26 , GLU E:50 , VAL E:75 , HIS E:114 , GLY F:389 , ASP F:390 , GLY F:413 , HIS F:414 , ILE F:415 , GLY F:439 , ASP F:440 , GLY F:441 , SER F:442 , ASN F:467 , GLY F:469 , TYR F:470 , THR F:471 , ILE F:472 , GLU F:473 , MG F:569 , HOH F:2450 , HOH F:2452 , HOH F:2497 , HOH F:2606	BINDING SITE FOR RESIDUE TPU F 600

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC_ZYMMO	423-442	4	A:423-442 B:423-442 E:423-442 F:423-442

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC_ZYMMO	423-442	4	A:423-442 B:423-442 E:423-442 F:423-442

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC_ZYMMO	423-442	2	A:423-442 B:423-442 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC_ZYMMO	423-442	2	- - E:423-442 F:423-442

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC_ZYMMO	423-442	2	A:423-442 - - F:423-442

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	PDC_ZYMMO	423-442	2	- B:423-442 E:423-442 -

(no "Exon" information available for 2WVG)

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:565
 aligned with PDC_ZYMMO | P06672 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:565
                                    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     
            PDC_ZYMMO     2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
               SCOP domains d2wvga1 A:2-187 automated matches                                                                                                                                                         d2wvga2 A:188-362 automated matches                                                                                                                                            d2wvga3 A:363-566 automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2wvgA01 A:2-186  [code=3.40.50.970, no name defined]                                                                                                                                     -2wvgA02 A:188-350 TPP-binding domain                                                                                                                               ----2wvgA03 A:355-548  [code=3.40.50.970, no name defined]                                                                                                                                            ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..ee.ee..hhhhhh....hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhh.................hhhhhhhhhhh.....eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvg A   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    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:565
 aligned with PDC_ZYMMO | P06672 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:565
                                    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     
            PDC_ZYMMO     2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
               SCOP domains d2wvgb1 B:2-187 automated matches                                                                                                                                                         d2wvgb2 B:188-362 automated matches                                                                                                                                            d2wvgb3 B:363-566 automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2wvgB01 B:2-186  [code=3.40.50.970, no name defined]                                                                                                                                     -2wvgB02 B:188-350 TPP-binding domain                                                                                                                               ----2wvgB03 B:355-548  [code=3.40.50.970, no name defined]                                                                                                                                            ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..ee.ee..hhhhhh....hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhh.................hhhhhhhhhhh.....eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh.......hhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvg B   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    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 E from PDB  Type:PROTEIN  Length:565
 aligned with PDC_ZYMMO | P06672 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:565
                                    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     
            PDC_ZYMMO     2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
               SCOP domains d2wvge1 E:2-187 automated matches                                                                                                                                                         d2wvge2 E:188-362 automated matches                                                                                                                                            d2wvge3 E:363-566 automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2wvgE01 E:2-186  [code=3.40.50.970, no name defined]                                                                                                                                     -2wvgE02 E:188-350 TPP-binding domain                                                                                                                               ----2wvgE03 E:355-548  [code=3.40.50.970, no name defined]                                                                                                                                            ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..ee.ee..hhhhhh....hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhh.................hhhhhhhhhhh.....eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvg E   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    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 F from PDB  Type:PROTEIN  Length:565
 aligned with PDC_ZYMMO | P06672 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:565
                                    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     
            PDC_ZYMMO     2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
               SCOP domains d2wvgf1 F:2-187 automated matches                                                                                                                                                         d2wvgf2 F:188-362 automated matches                                                                                                                                            d2wvgf3 F:363-566 automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2wvgF01 F:2-186  [code=3.40.50.970, no name defined]                                                                                                                                     -2wvgF02 F:188-350 TPP-binding domain                                                                                                                               ----2wvgF03 F:355-548  [code=3.40.50.970, no name defined]                                                                                                                                            ------------------ CATH domains
           Pfam domains (1) -TPP_enzyme_N-2wvgF09 F:3-179                                                                                                                                                     -------------------TPP_enzyme_M-2wvgF01 F:199-360                                                                                                                                    --------------------------TPP_enzyme_C-2wvgF05 F:387-537                                                                                                                         ----------------------------- Pfam domains (1)
           Pfam domains (2) -TPP_enzyme_N-2wvgF10 F:3-179                                                                                                                                                     -------------------TPP_enzyme_M-2wvgF02 F:199-360                                                                                                                                    --------------------------TPP_enzyme_C-2wvgF06 F:387-537                                                                                                                         ----------------------------- Pfam domains (2)
           Pfam domains (3) -TPP_enzyme_N-2wvgF11 F:3-179                                                                                                                                                     -------------------TPP_enzyme_M-2wvgF03 F:199-360                                                                                                                                    --------------------------TPP_enzyme_C-2wvgF07 F:387-537                                                                                                                         ----------------------------- Pfam domains (3)
           Pfam domains (4) -TPP_enzyme_N-2wvgF12 F:3-179                                                                                                                                                     -------------------TPP_enzyme_M-2wvgF04 F:199-360                                                                                                                                    --------------------------TPP_enzyme_C-2wvgF08 F:387-537                                                                                                                         ----------------------------- Pfam domains (4)
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..ee.ee..hhhhhh....hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhh.................hhhhhhhhhhh.....eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvg F   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    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)

Zymomonas mobilis [TaxId: 542] (4)

1a	d2wvga2	A:188-362
1b	d2wvgb2	B:188-362
1c	d2wvge2	E:188-362
1d	d2wvgf2	F:188-362

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)

Zymomonas mobilis [TaxId: 542] (4)

2a	d2wvga1	A:2-187
2b	d2wvga3	A:363-566
2c	d2wvgb1	B:2-187
2d	d2wvgb3	B:363-566
2e	d2wvge1	E:2-187
2f	d2wvge3	E:363-566
2g	d2wvgf1	F:2-187
2h	d2wvgf3	F:363-566

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)

Zymomonas mobilis. Organism_taxid: 542. (4)

1a	2wvgA03	A:355-548
1b	2wvgB03	B:355-548
1c	2wvgE03	E:355-548
1d	2wvgA01	A:2-186
1e	2wvgB01	B:2-186
1f	2wvgE01	E:2-186
1g	2wvgF01	F:2-186
1h	2wvgF03	F:355-548

Homologous Superfamily: TPP-binding domain (120)

Zymomonas mobilis. Organism_taxid: 542. (4)

2a	2wvgA02	A:188-350
2b	2wvgB02	B:188-350
2c	2wvgE02	E:188-350
2d	2wvgF02	F:188-350

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_DHS (82)

Family: TPP_enzyme_M (50)

Zymomonas mobilis (5)

1a	TPP_enzyme_M-2wvgF01	F:199-360
1b	TPP_enzyme_M-2wvgF02	F:199-360
1c	TPP_enzyme_M-2wvgF03	F:199-360
1d	TPP_enzyme_M-2wvgF04	F:199-360

Clan: THDP-binding (106)

Family: TPP_enzyme_C (54)

Zymomonas mobilis (5)

2a	TPP_enzyme_C-2wvgF05	F:387-537
2b	TPP_enzyme_C-2wvgF06	F:387-537
2c	TPP_enzyme_C-2wvgF07	F:387-537
2d	TPP_enzyme_C-2wvgF08	F:387-537

Family: TPP_enzyme_N (54)

Zymomonas mobilis (5)

3a	TPP_enzyme_N-2wvgF09	F:3-179
3b	TPP_enzyme_N-2wvgF10	F:3-179
3c	TPP_enzyme_N-2wvgF11	F:3-179
3d	TPP_enzyme_N-2wvgF12	F:3-179

Asymmetric Unit(hide GO term definitions)

Chain A,B,E,F (PDC_ZYMMO | P06672)


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
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	2wvg
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	4.1.1.1
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UniProtKB/Swiss-Prot
	PDC_ZYMMO \| P06672	:	1zpd 2wva 2wvh 3oe1 4zp1

1zpd	PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS
2wvh	STRUCTURAL INSIGHTS INTO THE PRE-REACTION STATE OF PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

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

Classification and Annotation

SCOP Domains (2, 12)

CATH Domains (2, 12)

Pfam Domains (3, 12)

Gene Ontology (7, 7)

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