PDBsum entry 2gub

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Isomerase PDB id
Jmol PyMol
Protein chain
385 a.a. *
Waters ×374
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of metal free d-xylose isomerase.
Structure: Xylose isomerase. Chain: a. Ec:
Source: Streptomyces rubiginosus. Organism_taxid: 1929. Other_details: purified enzyme obtained as gift from clinto products, clinton, ia.
Biol. unit: Tetramer (from PDB file)
1.80Å     R-factor:   0.161     R-free:   0.193
Authors: H.L.Carrell,A.K.Katz,J.P.Glusker
Key ref:
A.K.Katz et al. (2006). Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction. Proc Natl Acad Sci U S A, 103, 8342-8347. PubMed id: 16707576 DOI: 10.1073/pnas.0602598103
29-Apr-06     Release date:   16-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P24300  (XYLA_STRRU) -  Xylose isomerase
388 a.a.
385 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
= D-xylulose
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     isomerase activity     3 terms  


    Key reference    
DOI no: 10.1073/pnas.0602598103 Proc Natl Acad Sci U S A 103:8342-8347 (2006)
PubMed id: 16707576  
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.
A.K.Katz, X.Li, H.L.Carrell, B.L.Hanson, P.Langan, L.Coates, B.P.Schoenborn, J.P.Glusker, G.J.Bunick.
Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.
  Selected figure(s)  
Figure 3.
Fig. 3. Spatial relationship of glucose substrate to His-54. (Left) Neutron map (1.8-Å resolution) showing His-54 with coordinates of glucose from an x-ray study (1.6-Å resolution; PDB ID code 1XIF) shown by yellow lines. Nuclear density is shown for Asp-57, His-54, and heavy water W1022. (Right) Model with W1022 superimposed on the site of a metal ion-bound cyclic glucose. His-54 NE2 provides a proton to the water molecule (W1022 at 2.67 Å) in the absence of substrate. Presumably, when the cyclic form of the sugar substrate is present, the water molecule is displaced, and a hydrogen bond (2.68 Å) is formed between His-54 NE2 and O5 of the sugar. This result shows a possible mode of protonation required for substrate ring opening. The metal ion, M1, that binds the other end of the cyclic glucose, is shown at the bottom of the diagrams.
Figure 5.
Fig. 5. Environment of proposed catalytic water (shown with heavy black bonds). (a) Nuclear density (2F[o] – F[c]). (b) Atomic arrangement in the 1.8-Å-resolution neutron map. Both diagrams show the water molecule (with an elongated shape indicating two protons) and the two metal ion-carboxylate-water motifs. In the electron-density map (data not shown), two possible conformations exist for Asp-257, one of which agrees with the nuclear-density results shown here.
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20541506 A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, and P.Langan (2010).
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
  Structure, 18, 688-699.
PDB codes: 3kbm 3kbn 3kbs 3kbv 3kbw 3kcl 3kco
20541500 B.C.Bennett, and M.Yeager (2010).
The lighter side of a sweet reaction.
  Structure, 18, 657-659.  
20088877 H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, and S.Kamitori (2010).
Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures.
  FEBS J, 277, 1045-1057.
PDB codes: 3itl 3ito 3itt 3itv 3itx 3ity 3iud 3iuh 3iui
  20383004 M.M.Blum, S.J.Tomanicek, H.John, B.L.Hanson, H.Rüterjans, B.P.Schoenborn, P.Langan, and J.C.Chen (2010).
X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 379-385.
PDB code: 3kgg
19136630 M.M.Blum, M.Mustyakimov, H.Rüterjans, K.Kehe, B.P.Schoenborn, P.Langan, and J.C.Chen (2009).
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
  Proc Natl Acad Sci U S A, 106, 713-718.
PDB code: 3byc
  19407386 S.Z.Fisher, A.Y.Kovalevsky, J.F.Domsic, M.Mustyakimov, D.N.Silverman, R.McKenna, and P.Langan (2009).
Preliminary joint neutron and X-ray crystallographic study of human carbonic anhydrase II.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 495-498.  
  19255494 W.R.Novak, A.G.Moulin, M.P.Blakeley, I.Schlichting, G.A.Petsko, and D.Ringe (2009).
A preliminary neutron diffraction study of gamma-chymotrypsin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 317-320.  
18578508 A.Y.Kovalevsky, A.K.Katz, H.L.Carrell, L.Hanson, M.Mustyakimov, S.Z.Fisher, L.Coates, B.P.Schoenborn, G.J.Bunick, J.P.Glusker, and P.Langan (2008).
Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose.
  Biochemistry, 47, 7595-7597.
PDB code: 3cwh
  18391424 A.Y.Kovalevsky, T.Chatake, N.Shibayama, S.Y.Park, T.Ishikawa, M.Mustyakimov, S.Z.Fisher, P.Langan, and Y.Morimoto (2008).
Preliminary time-of-flight neutron diffraction study of human deoxyhemoglobin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 270-273.  
18566512 B.C.Bennett, A.S.Gardberg, M.D.Blair, and C.G.Dealwis (2008).
On the determinants of amide backbone exchange in proteins: a neutron crystallographic comparative study.
  Acta Crystallogr D Biol Crystallogr, 64, 764-783.  
18421142 P.Langan, Z.Fisher, A.Kovalevsky, M.Mustyakimov, A.Sutcliffe Valone, C.Unkefer, M.J.Waltman, L.Coates, P.D.Adams, P.V.Afonine, B.Bennett, C.Dealwis, and B.P.Schoenborn (2008).
Protein structures by spallation neutron crystallography.
  J Synchrotron Radiat, 15, 215-218.  
  17183172 M.M.Blum, A.Koglin, H.Rüterjans, B.Schoenborn, P.Langan, and J.C.Chen (2007).
Preliminary time-of-flight neutron diffraction study on diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 42-45.  
18007033 S.Z.Fisher, S.Anderson, R.Henning, K.Moffat, P.Langan, P.Thiyagarajan, and A.J.Schultz (2007).
Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP).
  Acta Crystallogr D Biol Crystallogr, 63, 1178-1184.
PDB code: 2qws
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.