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(-) Description

Title :  HUMAN TRANSKETOLASE IN COVALENT COMPLEX WITH DONOR KETOSE D-XYLULOSE-5-PHOSPHATE, CRYSTAL 1
 
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 :  0.97
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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2DX51Ligand/IonD-XYLITOL-5-PHOSPHATE
3EDO9Ligand/Ion1,2-ETHANEDIOL
4TDP1Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DX52Ligand/IonD-XYLITOL-5-PHOSPHATE
3EDO18Ligand/Ion1,2-ETHANEDIOL
4TDP2Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:155 , ASN A:185 , LEU A:187 , TDP A:1011 , HOH A:7001BINDING SITE FOR RESIDUE CA A 1001
02AC2SOFTWAREPRO A:63 , ASN A:68 , ASP A:69 , ARG A:70 , PHE A:71 , ARG A:379 , HOH A:7185 , HOH A:7887BINDING SITE FOR RESIDUE EDO A 1002
03AC3SOFTWAREPHE A:71 , VAL A:72 , LEU A:73 , LEU A:82 , PHE A:117 , HOH A:7043 , HOH A:7059 , HOH A:7081BINDING SITE FOR RESIDUE EDO A 1003
04AC4SOFTWARETYR A:564 , ALA A:588 , ASN A:590 , HOH A:7035 , HOH A:7051 , HOH A:7134 , HOH A:7250BINDING SITE FOR RESIDUE EDO A 1004
05AC5SOFTWAREARG A:21 , SER A:25 , ALA A:84 , ALA A:87 , GLU A:88 , GLU A:94 , LEU A:97 , LYS A:283 , HOH A:7317 , HOH A:7643BINDING SITE FOR RESIDUE EDO A 1005
06AC6SOFTWARELEU A:92 , ASP A:106 , LEU A:107 , GLN A:115 , HOH A:7117 , HOH A:7124 , HOH A:7162BINDING SITE FOR RESIDUE EDO A 1006
07AC7SOFTWAREGLN A:10 , LYS A:11 , ASN A:590 , ARG A:591 , HOH A:7309 , HOH A:7885BINDING SITE FOR RESIDUE EDO A 1007
08AC8SOFTWAREALA A:33 , LEU A:100 , ARG A:101 , LYS A:102 , GLU A:423 , LYS A:597 , HOH A:7104 , HOH A:7916 , HOH A:7935 , HOH A:7948BINDING SITE FOR RESIDUE EDO A 1008
09AC9SOFTWARELEU A:158 , TRP A:164 , LEU A:195 , ARG A:205 , HOH A:7040 , HOH A:7149 , HOH A:7803 , HOH A:7866BINDING SITE FOR RESIDUE EDO A 1009
10BC1SOFTWARETYR A:137 , TYR A:141 , TYR A:173 , HOH A:7364 , HOH A:7500 , HOH A:7728BINDING SITE FOR RESIDUE EDO A 1010
11BC2SOFTWARESER 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 , CA A:1001 , DX5 A:1012 , HOH A:7001BINDING SITE FOR RESIDUE TDP A 1011
12BC3SOFTWAREHIS A:37 , HIS A:77 , HIS A:110 , 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:1011 , HOH A:7067 , HOH A:7102 , HOH A:7121 , HOH A:7273 , HOH A:7297 , HOH A:7427 , HOH A:7738 , HOH A:7957BINDING SITE FOR RESIDUE DX5 A 1012

(-) SS Bonds  (0, 0)

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

(-) 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 4KXV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KXV)

(-) 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: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.....................hhhhhhhhhhhhhh.....................................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..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxv 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
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  4kxv
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  2.2.1.1
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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