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Title :   THE STRUCTURE OF HUMAN TRANSKETOLASE

Authors :   C. Parthier, K. Tittmann

Date :   23 Apr 10 (Deposition) - 28 Jul 10 (Release) - 20 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Thiamin Diphosphate Tpp Thdp Enzyme Catalysis Sugar Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Mitschke, C. Parthier, K. Schroder-Tittmann, J. Coy, S. Ludtke, K. Tittmann
The Crystal Structure Of Human Transketolase And New Insights Into Its Mode Of Action.
J. Biol. Chem. V. 285 31559 2010
PubMed-ID: 20667822 | Reference-DOI: 10.1074/JBC.M110.149955

Molecule 1 - TRANSKETOLASE
	Chains	:	A
	EC Number	:	2.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TKT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TK

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION
4	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (2, 22)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	20	Ligand/Ion	1,2-ETHANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CA A:1 , SER A:40 , LYS A:75 , HIS A:77 , GLY A:123 , SER A:124 , LEU A:125 , GLY A:154 , ASP A:155 , GLY A:156 , GLU A:157 , GLU A:160 , ASN A:185 , LEU A:187 , GLY A:188 , GLN A:189 , LYS A:244 , HIS A:258 , ASP A:341 , ILE A:364 , GLU A:366 , PHE A:392 , ARG A:395 , GLN A:428 , HOH A:629	BINDING SITE FOR RESIDUE TPP A 700
02	AC2	SOFTWARE	ASP A:155 , ASN A:185 , LEU A:187 , HOH A:629 , TPP A:700	BINDING SITE FOR RESIDUE CA A 1
03	AC3	SOFTWARE	GLN A:127 , SER A:371 , VAL A:374 , GLN A:399 , MET A:402 , ALA A:403 , HOH A:933	BINDING SITE FOR RESIDUE EDO A 619
04	AC4	SOFTWARE	PRO A:441 , LYS A:538 , TYR A:563 , TYR A:564 , GLU A:565 , VAL A:589 , ASN A:590 , HOH A:792 , HOH A:981	BINDING SITE FOR RESIDUE EDO A 2
05	AC5	SOFTWARE	LEU A:158 , SER A:159 , TRP A:164 , GLU A:165 , ALA A:168 , PHE A:209 , EDO A:624	BINDING SITE FOR RESIDUE EDO A 620
06	AC6	SOFTWARE	GLN A:189 , SER A:256 , TRP A:257 , HIS A:258 , ASN A:344 , HOH A:688 , HOH A:924	BINDING SITE FOR RESIDUE EDO A 621
07	AC7	SOFTWARE	TYR A:564 , ALA A:588 , ASN A:590 , HOH A:678 , HOH A:761 , HOH A:766 , HOH A:968	BINDING SITE FOR RESIDUE EDO A 622
08	AC8	SOFTWARE	ARG A:21 , ALA A:84 , GLU A:88 , GLU A:94 , LEU A:97	BINDING SITE FOR RESIDUE EDO A 623
09	AC9	SOFTWARE	LEU A:158 , TRP A:164 , ARG A:205 , PHE A:209 , EDO A:620 , HOH A:644	BINDING SITE FOR RESIDUE EDO A 624
10	BC1	SOFTWARE	PRO A:63 , ASN A:68 , ASP A:69 , ARG A:70 , PHE A:71 , ARG A:379 , HOH A:835	BINDING SITE FOR RESIDUE EDO A 625
11	BC2	SOFTWARE	ALA A:14 , ASN A:590 , ARG A:591 , HOH A:1029	BINDING SITE FOR RESIDUE EDO A 626
12	BC3	SOFTWARE	PHE A:71 , VAL A:72 , LEU A:73 , LEU A:82 , PHE A:117 , HOH A:666 , HOH A:670 , HOH A:717	BINDING SITE FOR RESIDUE EDO A 627
13	BC4	SOFTWARE	ASN A:411 , ALA A:461 , THR A:464 , CYS A:468 , HOH A:657 , HOH A:691	BINDING SITE FOR RESIDUE NA A 628

(no "SS Bond" information available for 3MOS)

Asymmetric Unit

No.	Residues
1	Lys A:538	-	Pro A:539

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052634	I	181	V	TKT_HUMAN	Polymorphism	17052920	A	I	181	V
2	UniProt	VAR_077030	R	318	C	TKT_HUMAN	Disease (SDDHD)	782092363	A	R	318	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052634	I	181	V	TKT_HUMAN	Polymorphism	17052920	A	I	181	V
2	UniProt	VAR_077030	R	318	C	TKT_HUMAN	Disease (SDDHD)	782092363	A	R	318	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSKETOLASE_1	PS00801	Transketolase signature 1.	TKT_HUMAN	23-43	1	A:23-43
2	TRANSKETOLASE_2	PS00802	Transketolase signature 2.	TKT_HUMAN	422-438	1	A:422-438

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSKETOLASE_1	PS00801	Transketolase signature 1.	TKT_HUMAN	23-43	2	A:23-43
2	TRANSKETOLASE_2	PS00802	Transketolase signature 2.	TKT_HUMAN	422-438	2	A:422-438

(no "Exon" information available for 3MOS)

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:616
 aligned with TKT_HUMAN | P29401 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:616
                                    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      
            TKT_HUMAN     3 SYHKPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQAKHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPRSGKPAELLKMFGIDRDAIAQAVRG 618
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Transketolase_N-3mosA02 A:14-304                                                                                                                                                                                                                                                                   --------Transket_pyr-3mosA01 A:313-478                                                                                                                                        -----------Transketolase_C-3mosA03 A:490-612                                                                                          ------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............eeee.hhhhhhhhhhhhhhh...hhhhhhhh..........................hhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeee.............hhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.....eeeeee.....................hhhhhhhhhhhhhhh......................................hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhh...eeeeee..hhhhh..hhhhh..hhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeee.....................eeee....eeeeee..hhhhhhhhhhhhhhhh...eeeeee..eee..hhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhh.....eeeeeee.......hhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V----------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------TRANSKETOLASE_1      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mos A   3 SYHKPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQAKHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPRSGKPAELLKMFGIDRDAIAQAVRG 618
                                    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

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 '\|'

(no "SCOP Domain" information available for 3MOS)

(no "CATH Domain" information available for 3MOS)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: THDP-binding (106)

Family: Transket_pyr (45)

Homo sapiens (Human) (16)

Transket_pyr-3mosA01

A:313-478

Family: Transketolase_N (22)

Homo sapiens (Human) (2)

Transketolase_N-3mosA02

A:14-304

Clan: no clan defined [family: Transketolase_C] (40)

Family: Transketolase_C (40)

Homo sapiens (Human) (16)

Transketolase_C-3mosA03

A:490-612

Asymmetric Unit(hide GO term definitions)

Chain A (TKT_HUMAN | P29401)

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:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0046166	glyceraldehyde-3-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
	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.
	GO:0009052	pentose-phosphate shunt, non-oxidative branch	The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
	GO:0040008	regulation of growth	Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
	GO:0005999	xylulose biosynthetic process	The chemical reactions and pathways resulting in the formation of xylulose, the ketopentose threo-2-pentulose.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:538 - Pro A:539	[ RasMol ]

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	3mos
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	TKT_HUMAN \| P29401
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	TKT_HUMAN \| P29401	:	3ooy 4kxu 4kxv 4kxw 4kxx 4kxy

(no "Related Entries Specified in the PDB File" available for 3MOS)

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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