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(-) Description

Title :  HUMAN TRANSKETOLASE IN COVALENT COMPLEX WITH DONOR KETOSE D-SEDOHEPTULOSE-7-PHOSPHATE
 
Authors :  P. Neumann, S. Luedtke, R. Ficner, K. Tittmann
Date :  28 May 13  (Deposition) - 21 Aug 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.03
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Thiamin Diphosphate, Enzyme Catalysis, Pentose Phosphate Pathway, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ludtke, P. Neumann, K. M. Erixon, F. Leeper, R. Kluger, R. Ficner, K. Tittmann
Sub-Angstrom-Resolution Crystallography Reveals Physical Distortions That Enhance Reactivity Of A Covalent Enzymatic Intermediate.
Nat Chem V. 5 762 2013
PubMed-ID: 23965678  |  Reference-DOI: 10.1038/NCHEM.1728

(-) Compounds

Molecule 1 - TRANSKETOLASE
    Chains: A
    EC Number: 2.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TKT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TK

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
11Y71Ligand/Ion(2R,3R,4S,5R,6S)-2,3,4,5,6,7-HEXAHYDROXYHEPTYLDIHYDROGEN PHOSPHATE
2EDO12Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
5TDP1Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
11Y72Ligand/Ion(2R,3R,4S,5R,6S)-2,3,4,5,6,7-HEXAHYDROXYHEPTYLDIHYDROGEN PHOSPHATE
2EDO24Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5TDP2Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:37 , HIS A:77 , HIS A:110 , GLY A:123 , GLN A:189 , HIS A:258 , ARG A:318 , SER A:345 , PHE A:389 , HIS A:416 , ASP A:424 , GLN A:428 , ARG A:474 , TDP A:1002 , HOH A:8065 , HOH A:8074 , HOH A:8196 , HOH A:8310 , HOH A:8387 , HOH A:8413 , HOH A:8573BINDING SITE FOR RESIDUE 1Y7 A 1001
02AC2SOFTWARESER 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 , 1Y7 A:1001 , MG A:1013 , HOH A:8446BINDING SITE FOR RESIDUE TDP A 1002
03AC3SOFTWAREVAL A:120 , GLN A:127 , ALA A:131 , SER A:371 , VAL A:374 , GLN A:399 , MET A:402 , ALA A:403 , HOH A:8199BINDING SITE FOR RESIDUE EDO A 1003
04AC4SOFTWARELEU A:92 , ASP A:106 , LEU A:107 , GLN A:115 , HOH A:8116 , HOH A:8191 , HOH A:8193BINDING SITE FOR RESIDUE EDO A 1004
05AC5SOFTWARELEU A:158 , SER A:159 , TRP A:164 , GLU A:165 , PHE A:209 , EDO A:1009BINDING SITE FOR RESIDUE EDO A 1005
06AC6SOFTWAREGLN A:10 , ASN A:590 , ARG A:591 , HOH A:8213 , HOH A:8511BINDING SITE FOR RESIDUE EDO A 1006
07AC7SOFTWAREARG A:21 , ALA A:84 , ALA A:87 , GLU A:88 , GLU A:94 , LEU A:97 , LYS A:283 , HOH A:8186 , HOH A:8509 , HOH A:8576BINDING SITE FOR RESIDUE EDO A 1007
08AC8SOFTWAREGLN A:189 , SER A:256 , TRP A:257 , HIS A:258 , LYS A:260 , ASN A:344 , HOH A:8092 , HOH A:8346 , HOH A:8659BINDING SITE FOR RESIDUE EDO A 1008
09AC9SOFTWARELEU A:158 , SER A:159 , TRP A:164 , LEU A:195 , TYR A:202 , ARG A:205 , PHE A:209 , EDO A:1005 , HOH A:8072 , HOH A:8095 , HOH A:8125BINDING SITE FOR RESIDUE EDO A 1009
10BC1SOFTWARETYR A:564 , ALA A:588 , ASN A:590 , HOH A:8053 , HOH A:8079 , HOH A:8359 , HOH A:8470BINDING SITE FOR RESIDUE EDO A 1010
11BC2SOFTWAREPHE A:71 , VAL A:72 , LEU A:73 , LEU A:82 , PHE A:117 , HOH A:8003 , HOH A:8069 , HOH A:8108BINDING SITE FOR RESIDUE EDO A 1011
12BC3SOFTWAREPRO A:63 , ASN A:68 , ASP A:69 , ARG A:70 , PHE A:71 , ARG A:379 , HOH A:8224BINDING SITE FOR RESIDUE EDO A 1012
13BC4SOFTWAREASP A:155 , ASN A:185 , LEU A:187 , TDP A:1002 , HOH A:8446BINDING SITE FOR RESIDUE MG A 1013
14BC5SOFTWAREALA A:33 , ARG A:101 , GLU A:423 , LYS A:597 , HOH A:8190 , HOH A:8381 , HOH A:8579BINDING SITE FOR RESIDUE EDO A 1014
15BC6SOFTWAREASN A:411 , ALA A:461 , THR A:464 , CYS A:468 , HOH A:8062 , HOH A:8091BINDING SITE FOR RESIDUE NA A 1015
16BC7SOFTWAREPRO A:441 , LYS A:538 , TYR A:563 , TYR A:564 , GLU A:565 , VAL A:589 , ASN A:590 , HOH A:8150 , HOH A:8485 , HOH A:8638BINDING SITE FOR RESIDUE EDO A 1016

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KXX)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KXX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KXX)

(-) Exons   (0, 0)

(no "Exon" information available for 4KXX)

(-) Sequences/Alignments

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:621
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............eeee.hhhhhhhhhhhhhhh...hhhhhhhh..........................hhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeee.............hhhhhhhhhhhh..eeeeee..hhhhhhhhhh......eeeeee.....................hhhhhhhhhhhhhhhh...................................eeehhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeeeehhhhh.hhhhhhhhhhh...eeeeee..hhhhh..hhhhh..hhhhhhhh....eee...hhhhhhhhhhhhhh...eeeee....eee..............eeee....eeeeee..hhhhhhhhhhhhhhhh...eeeeee..eee..hhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhh.....eeeeeee.......hhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxx A   1 MESYHKPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQAKHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPRSGKPAELLKMFGIDRDAIAQAVRGLIT 621
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4KXX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KXX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KXX)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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    Lys A:538 - Pro A:539   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        TKT_HUMAN | P29401: 3mos 3ooy 4kxu 4kxv 4kxw 4kxy

(-) Related Entries Specified in the PDB File

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