PDBsum entry 2nlx

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protein Protein-protein interface(s) links
Transferase PDB id
Protein chains
476 a.a. *
Waters ×158
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of the apo e. Coli xylulose kinase
Structure: Xylulose kinase. Chain: a, b. Synonym: xylulokinase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: xylb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.70Å     R-factor:   0.207     R-free:   0.254
Authors: E.Di Luccio,J.Voegtli,D.K.Wilson
Key ref:
E.Di Luccio et al. (2007). Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli. J Mol Biol, 365, 783-798. PubMed id: 17123542 DOI: 10.1016/j.jmb.2006.10.068
20-Oct-06     Release date:   14-Nov-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P09099  (XYLB_ECOLI) -  Xylulose kinase
484 a.a.
476 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Xylulokinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + D-xylulose = ADP + D-xylulose 5-phosphate
+ D-xylulose
+ D-xylulose 5-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   7 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1016/j.jmb.2006.10.068 J Mol Biol 365:783-798 (2007)
PubMed id: 17123542  
Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli.
E.Di Luccio, B.Petschacher, J.Voegtli, H.T.Chou, H.Stahlberg, B.Nidetzky, D.K.Wilson.
The primary metabolic route for D-xylose, the second most abundant sugar in nature, is via the pentose phosphate pathway after a two-step or three-step conversion to xylulose-5-phosphate. Xylulose kinase (XK; EC phosphorylates D-xylulose, the last step in this conversion. The apo and D-xylulose-bound crystal structures of Escherichia coli XK have been determined and show a dimer composed of two domains separated by an open cleft. XK dimerization was observed directly by a cryo-EM reconstruction at 36 A resolution. Kinetic studies reveal that XK has a weak substrate-independent MgATP-hydrolyzing activity, and phosphorylates several sugars and polyols with low catalytic efficiency. Binding of pentulose and MgATP to form the reactive ternary complex is strongly synergistic. Although the steady-state kinetic mechanism of XK is formally random, a path is preferred in which D-xylulose binds before MgATP. Modelling of MgATP binding to XK and the accompanying conformational change suggests that sugar binding is accompanied by a dramatic hinge-bending movement that enhances interactions with MgATP, explaining the observed synergism. A catalytic mechanism is proposed and supported by relevant site-directed mutants.
  Selected figure(s)  
Figure 3.
Figure 3. Sugar substrates used in substrate-specificity studies.
Figure 7.
Figure 7. The proposed catalytic mechanism for XK.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 783-798) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20406496 Y.Gu, Y.Ding, C.Ren, Z.Sun, D.A.Rodionov, W.Zhang, S.Yang, C.Yang, and W.Jiang (2010).
Reconstruction of xylose utilization pathway and regulons in Firmicutes.
  BMC Genomics, 11, 255.  
19819219 D.W.Pettigrew (2009).
Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase.
  Arch Biochem Biophys, 492, 29-39.  
18723107 O.Akinterinwa, and P.C.Cirino (2009).
Heterologous expression of D-xylulokinase from Pichia stipitis enables high levels of xylitol production by engineered Escherichia coli growing on xylose.
  Metab Eng, 11, 48-55.  
19043046 T.Ferguson, J.A.Soares, T.Lienard, G.Gottschalk, and J.A.Krzycki (2009).
RamA, a Protein Required for Reductive Activation of Corrinoid-dependent Methylamine Methyltransferase Reactions in Methanogenic Archaea.
  J Biol Chem, 284, 2285-2295.  
18346277 B.Petschacher, and B.Nidetzky (2008).
Altering the coenzyme preference of xylose reductase to favor utilization of NADH enhances ethanol yield from xylose in a metabolically engineered strain of Saccharomyces cerevisiae.
  Microb Cell Fact, 7, 9.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.