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(-) Description

Title :  HUMAN TRANSKETOLASE IN COMPLEX WITH THDP ANALOGUE (R)-2-(1,2-DIHYDROXYETHYL)-3-DEAZA-THDP
 
Authors :  P. Neumann, S. Luedtke, K. M. Erixon, F. Leeper, R. Kluger, R. Ficner, K.
Date :  28 May 13  (Deposition) - 21 Aug 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.26
Chains :  Asym./Biol. Unit :  A,B
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, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 35)

Asymmetric/Biological Unit (5, 35)
No.NameCountTypeFull Name
11U02Ligand/Ion2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1,2-DIHYDROXYETHYL]-3-METHYLTHIOPHEN-2-YL}ETHYLTRIHYDROGEN DIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3EDO27Ligand/Ion1,2-ETHANEDIOL
4NA2Ligand/IonSODIUM ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:423 , LYS A:597 , HOH A:8169 , HOH A:8187 , ALA B:33 , ARG B:101 , LYS B:102 , HOH B:1549BINDING SITE FOR RESIDUE EDO A 701
02AC2SOFTWAREARG A:21 , ALA A:84 , GLU A:88 , GLU A:94 , LEU A:97 , HOH A:8490 , HOH A:8519BINDING SITE FOR RESIDUE EDO A 702
03AC3SOFTWAREPHE A:71 , VAL A:72 , LEU A:73 , LEU A:82 , PHE A:117 , THR A:118 , HOH A:8072 , HOH A:8088 , HOH A:8130BINDING SITE FOR RESIDUE EDO A 703
04AC4SOFTWARETYR A:564 , ALA A:588 , ASN A:590 , HOH A:8071 , HOH A:8079 , HOH A:8137 , HOH A:8638BINDING SITE FOR RESIDUE EDO A 704
05AC5SOFTWAREGLN A:189 , SER A:256 , TRP A:257 , HIS A:258 , HOH A:8056 , HOH A:8357 , ASN B:344BINDING SITE FOR RESIDUE EDO A 705
06AC6SOFTWAREPRO A:63 , ASN A:68 , ASP A:69 , ARG A:70 , PHE A:71 , ARG A:379 , HOH A:8241BINDING SITE FOR RESIDUE EDO A 706
07AC7SOFTWAREASP A:155 , ASN A:185 , LEU A:187 , 1U0 A:709 , HOH A:8484BINDING SITE FOR RESIDUE CA A 707
08AC8SOFTWAREASN A:411 , ALA A:461 , THR A:464 , CYS A:468 , HOH A:8041 , HOH A:8042BINDING SITE FOR RESIDUE NA A 708
09AC9SOFTWAREHIS A:37 , SER A:40 , LYS A:75 , HIS A:77 , HIS A:110 , 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 , GLN A:189 , LYS A:244 , HIS A:258 , CA A:707 , HOH A:8053 , HOH A:8484 , HOH A:8571 , ILE B:364 , GLU B:366 , PHE B:392 , ARG B:395 , ASP B:424 , GLN B:428 , HOH B:1328BINDING SITE FOR RESIDUE 1U0 A 709
10BC1SOFTWAREGLU A:165 , PHE A:169 , CYS A:362 , ASN A:368 , HOH A:8281 , HOH A:8553 , SER B:159 , EDO B:1008BINDING SITE FOR RESIDUE EDO A 710
11BC2SOFTWAREGLN A:10 , HOH A:8273BINDING SITE FOR RESIDUE EDO A 711
12BC3SOFTWARETYR A:137 , TYR A:141 , TYR A:173 , HOH A:8383 , HOH A:8486 , HOH A:8688BINDING SITE FOR RESIDUE EDO A 712
13BC4SOFTWARELEU A:158 , SER A:159 , TRP A:164 , HOH A:8238 , HOH A:8437 , TRP B:164 , GLU B:165 , PHE B:209BINDING SITE FOR RESIDUE EDO A 713
14BC5SOFTWARELEU A:92 , LEU A:107 , GLN A:115 , HOH A:8082 , HOH A:8134 , HOH A:8183BINDING SITE FOR RESIDUE EDO A 714
15BC6SOFTWAREPRO A:475 , ASN A:477 , VAL A:510 , GLU A:514 , PRO A:598 , LEU A:602 , HOH A:8109 , HOH A:8340BINDING SITE FOR RESIDUE EDO A 715
16BC7SOFTWAREARG A:318 , SER A:345 , HIS A:416 , ARG A:474 , HOH A:8126 , HOH A:8284 , HOH A:8365 , HOH A:8659BINDING SITE FOR RESIDUE SO4 A 716
17BC8SOFTWAREGLN A:127 , ALA A:131 , SER A:371 , VAL A:374 , GLN A:399 , ALA A:403 , HOH A:8112BINDING SITE FOR RESIDUE EDO A 717
18BC9SOFTWAREASP A:333 , ARG A:358 , HOH A:8602BINDING SITE FOR RESIDUE EDO A 718
19CC1SOFTWAREARG B:21 , ALA B:84 , GLU B:88 , GLU B:94 , LEU B:97 , LYS B:283 , HOH B:1514 , HOH B:1615BINDING SITE FOR RESIDUE EDO B 1001
20CC2SOFTWARETYR B:564 , ALA B:588 , ASN B:590 , HOH B:1142 , HOH B:1169 , HOH B:1429 , HOH B:1454BINDING SITE FOR RESIDUE EDO B 1002
21CC3SOFTWAREPRO B:63 , ASN B:68 , ASP B:69 , ARG B:70 , PHE B:71 , ARG B:379 , HOH B:1705BINDING SITE FOR RESIDUE EDO B 1003
22CC4SOFTWAREPHE B:71 , VAL B:72 , LEU B:73 , LEU B:82 , PHE B:117 , THR B:118 , HOH B:1150 , HOH B:1160 , HOH B:1215BINDING SITE FOR RESIDUE EDO B 1004
23CC5SOFTWAREASN A:344 , GLN B:189 , SER B:256 , TRP B:257 , HIS B:258 , HOH B:1153 , HOH B:1374BINDING SITE FOR RESIDUE EDO B 1005
24CC6SOFTWAREASP A:341 , ILE A:364 , GLU A:366 , PHE A:392 , ARG A:395 , ASP A:424 , GLN A:428 , HIS B:37 , SER B:40 , LYS B:75 , HIS B:77 , HIS B:110 , GLY B:123 , SER B:124 , LEU B:125 , GLY B:154 , ASP B:155 , GLY B:156 , GLU B:157 , GLU B:160 , ASN B:185 , LEU B:187 , GLN B:189 , LYS B:244 , HIS B:258 , CA B:1007 , HOH B:1101 , HOH B:1122 , HOH B:1320 , HOH B:1334BINDING SITE FOR RESIDUE 1U0 B 1006
25CC7SOFTWAREASP B:155 , ASN B:185 , LEU B:187 , 1U0 B:1006 , HOH B:1101BINDING SITE FOR RESIDUE CA B 1007
26CC8SOFTWARETRP A:164 , GLU A:165 , PHE A:209 , EDO A:710 , LEU B:158 , SER B:159 , TRP B:164 , EDO B:1009BINDING SITE FOR RESIDUE EDO B 1008
27CC9SOFTWARELEU B:158 , TRP B:164 , ARG B:205 , EDO B:1008 , HOH B:1172 , HOH B:1202BINDING SITE FOR RESIDUE EDO B 1009
28DC1SOFTWAREGLN B:10 , HOH B:1426BINDING SITE FOR RESIDUE EDO B 1010
29DC2SOFTWAREALA A:33 , ARG A:101 , LYS A:102 , HOH A:8546 , GLU B:423 , LYS B:597 , HOH B:1354 , HOH B:1455BINDING SITE FOR RESIDUE EDO B 1011
30DC3SOFTWARELEU B:92 , LEU B:107 , GLN B:115 , HOH B:1176 , HOH B:1189 , HOH B:1228BINDING SITE FOR RESIDUE EDO B 1012
31DC4SOFTWAREHOH A:8624 , ARG B:318 , SER B:345 , HIS B:416 , ARG B:474 , HOH B:1208 , HOH B:1299 , HOH B:1720 , HOH B:1724BINDING SITE FOR RESIDUE SO4 B 1013
32DC5SOFTWAREASN B:411 , ALA B:461 , THR B:464 , CYS B:468 , HOH B:1131 , HOH B:1166BINDING SITE FOR RESIDUE NA B 1014
33DC6SOFTWAREPRO A:441 , LYS A:538 , HOH A:8347 , HOH A:8652 , TYR B:563 , TYR B:564 , GLU B:565 , VAL B:589 , ASN B:590 , HOH B:1295 , HOH B:1381BINDING SITE FOR RESIDUE EDO B 1015
34DC7SOFTWAREGLN B:127 , ALA B:131 , SER B:371 , HOH B:1240BINDING SITE FOR RESIDUE EDO B 1016
35DC8SOFTWARETYR B:137 , TYR B:141 , TYR B:173 , HOH B:1421 , HOH B:1589 , HOH B:1680BINDING SITE FOR RESIDUE EDO B 1017

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:538 -Pro A:539
2Lys B:538 -Pro B:539

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KXY)

(-) 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:620
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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..hhhhhhhhhhh.....eeeeee.....................hhhhhhhhhhhhhhh....................................eeehhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhh...eeeeee..hhhhh..hhhhh..hhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeee....eee..............eeee....eeeeee..hhhhhhhhhhhhhhhh...eeeeee..eee..hhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhh.....eeeeeee.......hhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxy A   2 ESYHKPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQAKHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPRSGKPAELLKMFGIDRDAIAQAVRGLIT 621
                                    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       571       581       591       601       611       621


Chain B from PDB  Type:PROTEIN  Length:620
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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..hhhhhhhhhhh.....eeeeee.....................hhhhhhhhhhhhhhh....................................eeehhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhh...eeeeee..hhhhh..hhhhh..hhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeee....eee..............eeee....eeeeee..hhhhhhhhhhhhhhhhh..eeeeee..eee..hhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhh.....eeeeeee.......hhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxy B   2 ESYHKPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQAKHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPRSGKPAELLKMFGIDRDAIAQAVRGLIT 621
                                    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       571       581       591       601       611       621
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  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 4KXY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  4kxy
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  TKT_HUMAN | P29401
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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 4kxx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4KXY)