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(-) Description

Title :  SPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE
 
Authors :  G. Schneider, S. Koenig
Date :  07 Feb 94  (Deposition) - 30 Nov 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Konig, A. Schellenberger, H. Neef, G. Schneider
Specificity Of Coenzyme Binding In Thiamin Diphosphate-Dependent Enzymes. Crystal Structures Of Yeast Transketolase In Complex With Analogs Of Thiamin Diphosphate.
J. Biol. Chem. V. 269 10879 1994
PubMed-ID: 8144674
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2N1T2Ligand/Ion1'-DEAZO-THIAMIN DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:157 , ASN A:187 , ILE A:189 , N1T A:681BINDING SITE FOR RESIDUE CA A 682
2AC2SOFTWAREASP B:157 , ASN B:187 , ILE B:189 , N1T B:681BINDING SITE FOR RESIDUE CA B 682
3AC3SOFTWAREALA A:33 , HIS A:69 , GLY A:116 , PRO A:117 , LEU A:118 , ASP A:157 , GLY A:158 , GLU A:162 , ASN A:187 , ILE A:189 , THR A:190 , ILE A:191 , HIS A:263 , CA A:682 , ASP B:382 , ILE B:416 , GLU B:418 , TYR B:448 , HIS B:481BINDING SITE FOR RESIDUE N1T A 681
4AC4SOFTWAREASP A:382 , GLU A:418 , PHE A:445 , TYR A:448 , HIS B:69 , GLY B:116 , PRO B:117 , LEU B:118 , ASP B:157 , GLY B:158 , ASN B:187 , ILE B:189 , THR B:190 , ILE B:191 , ILE B:250 , HIS B:263 , CA B:682BINDING SITE FOR RESIDUE N1T B 681

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSKETOLASE_1PS00801 Transketolase signature 1.TKT1_YEAST16-36
 		  2A:16-36
B:16-36
2TRANSKETOLASE_2PS00802 Transketolase signature 2.TKT1_YEAST475-491
 		  2A:475-491
B:475-491

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR074C1YPR074C.1XVI:694835-6927932043TKT1_YEAST1-6806802A:3-680
B:3-680		678
678

(-) Sequences/Alignments

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 d1tkba1 A:3-337 Transketolase (TK), PP module                                                                                                                                                                                                                                                                                                  d1tkba2 A:338-534 Transketolase (TK), Pyr module                                                                                                                                                     d1tkba3 A:535-680 Transketolase (TK), C-domain                                                                                                     SCOP domains
               CATH domains 1tkbA01 A:3-331  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                     1tkbA02 A:332-543  [code=3.40.50.970, no name defined]                                                                                                                                                              1tkbA03 A:544-680  [code=3.40.50.920, no name defined]                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............eeee.....hhhhhhhhhh......hhhhh............................hhhhhhhhhhhhhhhhhhhh...........------hhhhh.hhhhhhhhhhhhh....eeeeeee................hhhhhhh...eeeee......hhhhhhhhhhhhh.....eeeeee.....................hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......................hhhhhhhhhhhh......eeeee...hhhh.......................eee....hhhhhhhhhhhhhh....eeeeeeehhhh.................eeeee.................hhhhhh.....eeehhhhhhhhhhhhhhhhh.....eeee.............hhhh....eeee......eeeee...hhhhhhhhhhhhhh....eeeee...hhhhhh..hhhhhhh......eeee.............eee..........hhhhhhhh...hhhhhhhhhhhhhhh............. Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------------------------------------------------------------------------eeeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 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
                 1tkb 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 d1tkbb1 B:3-337 Transketolase (TK), PP module                                                                                                                                                                                                                                                                                                  d1tkbb2 B:338-534 Transketolase (TK), Pyr module                                                                                                                                                     d1tkbb3 B:535-680 Transketolase (TK), C-domain                                                                                                     SCOP domains
               CATH domains 1tkbB01 B:3-331  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                     1tkbB02 B:332-543  [code=3.40.50.970, no name defined]                                                                                                                                                              1tkbB03 B:544-680  [code=3.40.50.920, no name defined]                                                                                    CATH domains
           Pfam domains (1) ----Transketolase_N-1tkbB03 B:7-339                                                                                                                                                                                                                                                                                                              --------------Transket_pyr-1tkbB01 B:354-533                                                                                                                                                      ------------Transketolase_C-1tkbB05 B:546-656                                                                              ------------------------ Pfam domains (1)
           Pfam domains (2) ----Transketolase_N-1tkbB04 B:7-339                                                                                                                                                                                                                                                                                                              --------------Transket_pyr-1tkbB02 B:354-533                                                                                                                                                      ------------Transketolase_C-1tkbB06 B:546-656                                                                              ------------------------ Pfam domains (2)
     Sec.struct. author (1) ...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............eeee.....hhhhhhhhhh......hhhhh............................hhhhhhhhhhhhhhhhhhhh...........------hhhhh.hhhhhhhhhhhhh....eeeeeee................hhhhhhh...eeeee......hhhhhhhhhhhhh.....eeeeee.....................hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......................hhhhhhhhhhhh......eeeee...hhhh.......................eee....hhhhhhhhhhhhhh....eeeeeeehhhh.................eeeee.................hhhhhh.....eeehhhhhhhhhhhhhhhhh.....eeee.............hhhh....eeee......eeeee...hhhhhhhhhhhhhh....eeeee...hhhhhh..hhhhhhh......eeee.............eee..........hhhhhhhh...hhhhhhhhhhhhhhh............. Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------------------------------------------------------------------------eeeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 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
                 1tkb 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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: THDP-binding (106)
(-)
Clan: no clan defined [family: Transketolase_C] (40)

(-) Gene Ontology  (8, 8)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TKT1_YEAST | P23254: 1ay0 1gpu 1ngs 1tka 1tkc 1trk

(-) Related Entries Specified in the PDB File

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