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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   TRANSKETOLASE COMPLEX WITH REACTION INTERMEDIATE

Authors :   E. Fiedler, S. Thorell, T. Sandalova, S. Koenig, G. Schneider

Date :   09 Nov 01 (Deposition) - 11 Feb 02 (Release) - 01 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

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

Keywords :   Transferase(Ketone Residues), Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Fiedler, S. Thorell, T. Sandalova, R. Golbik, S. Koenig, G. Schneider
Snapshot Of A Key Intermediate In Enzymatic Thiamin Catalysis: Crystal Structure Of The Alpha- Carbanion Of (Alpha, Beta-Dihydroxyethyl)-Thiamin Diphosphate In The Active Site Of Transketolase From Saccharomyces Cerevisiae.
Proc. Natl. Acad. Sci. Usa V. 99 591 2002
PubMed-ID: 11773632 | Reference-DOI: 10.1073/PNAS.022510999
(for further references see the PDB file header)

Molecule 1 - TRANSKETOLASE 1
	Chains	:	A, B
	EC Number	:	2.2.1.1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	TK 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	THD	2	Ligand/Ion	2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:157 , ASN A:187 , ILE A:189 , THD A:1682 , HOH A:2140	BINDING SITE FOR RESIDUE CA A1681
2	AC2	SOFTWARE	ASP B:157 , ASP B:185 , ASN B:187 , THD B:1682	BINDING SITE FOR RESIDUE CA B1681
3	AC3	SOFTWARE	ALA A:33 , HIS A:69 , HIS A:103 , GLY A:116 , PRO A:117 , LEU A:118 , ASP A:157 , GLY A:158 , GLU A:162 , ASN A:187 , ILE A:189 , ILE A:191 , HIS A:263 , CA A:1681 , HOH A:2049 , HOH A:2404 , HOH A:2405 , ASP B:382 , ILE B:416 , GLU B:418 , PHE B:442 , PHE B:445 , TYR B:448 , HIS B:481	BINDING SITE FOR RESIDUE THD A1682
4	AC4	SOFTWARE	ASP A:382 , GLU A:418 , PHE A:442 , PHE A:445 , TYR A:448 , HIS A:481 , ALA B:33 , HIS B:69 , HIS B:103 , GLY B:116 , LEU B:118 , ASP B:157 , GLY B:158 , GLU B:162 , ASN B:187 , ILE B:189 , THR B:190 , ILE B:191 , HIS B:263 , CA B:1681 , HOH B:2027 , HOH B:2058 , HOH B:2454	BINDING SITE FOR RESIDUE THD B1682

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

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSKETOLASE_1	PS00801	Transketolase signature 1.	TKT1_YEAST	16-36	2	A:16-36 B:16-36
2	TRANSKETOLASE_2	PS00802	Transketolase signature 2.	TKT1_YEAST	475-491	2	A:475-491 B:475-491

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPR074C	1	YPR074C.1	XVI:694835-692793	2043	TKT1_YEAST	1-680	680	2	A:3-680 B:3-680	678 678

Asymmetric/Biological 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:678
 aligned with TKT1_YEAST | P23254 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:678
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672        
           TKT1_YEAST     3 QFTDIDKLAVSTIRILAVDTVSKANSGHPGAPLGMAPAAHVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLHLTGYDLSIEDLKQFRQLGSRTPGHPEFELPGVEVTTGPLGQGISNAVGMAMAQANLAATYNKPGFTLSDNYTYVFLGDGCLQEGISSEASSLAGHLKLGNLIAIYDDNKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTLIKMTTTIGYGSLHAGSHSVHGAPLKADDVKQLKSKFGFNPDKSFVVPQEVYDHYQKTILKPGVEANNKWNKLFSEYQKKFPELGAELARRLSGQLPANWESKLPTYTAKDSAVATRKLSETVLEDVYNQLPELIGGSADLTPSNLTRWKEALDFQPPSSGSGNYSGRYIRYGIREHAMGAIMNGISAFGANYKPYGGTFLNFVSYAAGAVRLSALSGHPVIWVATHDSIGVGEDGPTHQPIETLAHFRSLPNIQVWRPADGNEVSAAYKNSLESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVANPDIILVATGSEVSLSVEAAKTLAAKNIKARVVSLPDFFTFDKQPLEYRLSVLPDNVPIMSVEVLATTCWGKYAHQSFGIDRFGASGKAPEVFKFFGFTPEGVAERAQKTIAFYKGDKLISPLKKAF 680
               SCOP domains d1gpua1 A:3-337 Transketolase (TK), PP module                                                                                                                                                                                                                                                                                                  d1gpua2 A:338-534 Transketolase (TK), Pyr module                                                                                                                                                     d1gpua3 A:535-680 Transketolase (TK), C-domain                                                                                                     SCOP domains
               CATH domains 1gpuA01 A:3-331  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                     1gpuA02 A:332-543  [code=3.40.50.970, no name defined]                                                                                                                                                              1gpuA03 A:544-680  [code=3.40.50.920, no name defined]                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhhh....hhhhhh...........................hhhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhhhhhh....eeeeeee..ee..ee.hhh...hhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh....eeeeee...........hhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh..........hhhhhhhhhhhhhh.....eeeee..hhhhhh.......ee.......ee....eee...hhhhhhhhhhhhhhhh...eeeeeeehhhhh.hhhhhhhhhhhh...eeeee..hhhhh.........hhhhhhhh....eee...hhhhhhhhhhhhhhh....eeee............hhhhhh...eeee......eeeee..hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhh.....eeee......hhhhh..eee.........hhhhhhhhh..hhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------TRANSKETOLASE_1      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-680 UniProt: 1-680 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1gpu A   3 QFTDIDKLAVSTIRILAVDTVSKANSGHPGAPLGMAPAAHVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLHLTGYDLSIEDLKQFRQLGSRTPGHPEFELPGVEVTTGPLGQGISNAVGMAMAQANLAATYNKPGFTLSDNYTYVFLGDGCLQEGISSEASSLAGHLKLGNLIAIYDDNKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTLIKMTTTIGYGSLHAGSHSVHGAPLKADDVKQLKSKFGFNPDKSFVVPQEVYDHYQKTILKPGVEANNKWNKLFSEYQKKFPELGAELARRLSGQLPANWESKLPTYTAKDSAVATRKLSETVLEDVYNQLPELIGGSADLTPSNLTRWKEALDFQPPSSGSGNYSGRYIRYGIREHAMGAIMNGISAFGANYKPYGGTFLNFVSYAAGAVRLSALSGHPVIWVATHDSIGVGEDGPTHQPIETLAHFRSLPNIQVWRPADGNEVSAAYKNSLESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVANPDIILVATGSEVSLSVEAAKTLAAKNIKARVVSLPDFFTFDKQPLEYRLSVLPDNVPIMSVEVLATTCWGKYAHQSFGIDRFGASGKAPEVFKFFGFTPEGVAERAQKTIAFYKGDKLISPLKKAF 680
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672

Chain B from PDB  Type:PROTEIN  Length:678
 aligned with TKT1_YEAST | P23254 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:678
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672        
           TKT1_YEAST     3 QFTDIDKLAVSTIRILAVDTVSKANSGHPGAPLGMAPAAHVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLHLTGYDLSIEDLKQFRQLGSRTPGHPEFELPGVEVTTGPLGQGISNAVGMAMAQANLAATYNKPGFTLSDNYTYVFLGDGCLQEGISSEASSLAGHLKLGNLIAIYDDNKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTLIKMTTTIGYGSLHAGSHSVHGAPLKADDVKQLKSKFGFNPDKSFVVPQEVYDHYQKTILKPGVEANNKWNKLFSEYQKKFPELGAELARRLSGQLPANWESKLPTYTAKDSAVATRKLSETVLEDVYNQLPELIGGSADLTPSNLTRWKEALDFQPPSSGSGNYSGRYIRYGIREHAMGAIMNGISAFGANYKPYGGTFLNFVSYAAGAVRLSALSGHPVIWVATHDSIGVGEDGPTHQPIETLAHFRSLPNIQVWRPADGNEVSAAYKNSLESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVANPDIILVATGSEVSLSVEAAKTLAAKNIKARVVSLPDFFTFDKQPLEYRLSVLPDNVPIMSVEVLATTCWGKYAHQSFGIDRFGASGKAPEVFKFFGFTPEGVAERAQKTIAFYKGDKLISPLKKAF 680
               SCOP domains d1gpub1 B:3-337 Transketolase (TK), PP module                                                                                                                                                                                                                                                                                                  d1gpub2 B:338-534 Transketolase (TK), Pyr module                                                                                                                                                     d1gpub3 B:535-680 Transketolase (TK), C-domain                                                                                                     SCOP domains
               CATH domains 1gpuB01 B:3-331  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                     1gpuB02 B:332-543  [code=3.40.50.970, no name defined]                                                                                                                                                              1gpuB03 B:544-680  [code=3.40.50.920, no name defined]                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhhh....hhhhhh...........................hhhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhhhhhh....eeeeeee..ee..ee.hhh...hhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh....eeeeee...........hhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh..........hhhhhhhhhhhhhh.....eeeee..hhhhhh.......ee.......ee....eee...hhhhhhhhhhhhhhhh...eeeeeeehhhhh.hhhhhhhhhhhh...eeeee..hhhhhhhh......hhhhhhhh....eee...hhhhhhhhhhhhhhh....eeee............hhhhhh...eeee......eeeee..hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhh.....eeee......hhhhh..eee.........hhhhhhhhh..hhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------TRANSKETOLASE_1      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-680 UniProt: 1-680 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1gpu B   3 QFTDIDKLAVSTIRILAVDTVSKANSGHPGAPLGMAPAAHVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLHLTGYDLSIEDLKQFRQLGSRTPGHPEFELPGVEVTTGPLGQGISNAVGMAMAQANLAATYNKPGFTLSDNYTYVFLGDGCLQEGISSEASSLAGHLKLGNLIAIYDDNKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTLIKMTTTIGYGSLHAGSHSVHGAPLKADDVKQLKSKFGFNPDKSFVVPQEVYDHYQKTILKPGVEANNKWNKLFSEYQKKFPELGAELARRLSGQLPANWESKLPTYTAKDSAVATRKLSETVLEDVYNQLPELIGGSADLTPSNLTRWKEALDFQPPSSGSGNYSGRYIRYGIREHAMGAIMNGISAFGANYKPYGGTFLNFVSYAAGAVRLSALSGHPVIWVATHDSIGVGEDGPTHQPIETLAHFRSLPNIQVWRPADGNEVSAAYKNSLESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVANPDIILVATGSEVSLSVEAAKTLAAKNIKARVVSLPDFFTFDKQPLEYRLSVLPDNVPIMSVEVLATTCWGKYAHQSFGIDRFGASGKAPEVFKFFGFTPEGVAERAQKTIAFYKGDKLISPLKKAF 680
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672

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

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.920, no name defined] (73)

Baker's yeast (Saccharomyces cerevisiae) (7)

1a	1gpuA03	A:544-680
1b	1gpuB03	B:544-680

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

Baker's yeast (Saccharomyces cerevisiae) (17)

2a	1gpuA02	A:332-543
2b	1gpuB02	B:332-543
2c	1gpuA01	A:3-331
2d	1gpuB01	B:3-331

(no "Pfam Domain" information available for 1GPU)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TKT1_YEAST | P23254)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0004802	transketolase activity	Catalysis of the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a ketose phosphate donor to an aldose phosphate acceptor.
biological process
	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:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	TKT1_YEAST \| P23254	:	1ay0 1ngs 1tka 1tkb 1tkc 1trk

1ay0	IDENTIFICATION OF CATALYTICALLY IMPORTANT RESIDUES IN YEAST TRANSKETOLASE
1ngs	COMPLEX OF TRANSKETOLASE WITH THIAMIN DIPHOSPHATE, CA2+ AND ACCEPTOR SUBSTRATE ERYTHROSE-4-PHOSPHATE
1tka	TRANSKETOLASE COMPLEXED WITH 3'-DEAZO-THIAMIN DIPHOSPHATE AND CALCIUM
1tkb	TRANSKETOLASE COMPLEXED WITH 1'-DEAZO-THIAMIN DIPHOSPHATE AND CALCIUM
1tkc	TRANSKETOLASE COMPLEXED WITH 6'-METHYL-THIAMIN DIPHOSPHATE AND CALCIUM
1trk	TRANSKETOLASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (1, 2)

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SCOP Domains (3, 6)

CATH Domains (2, 6)

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