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PDBsum entry 1rk2

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1rk2
Jmol
Contents
Protein chains
305 a.a. *
Ligands
RIB ×4
ALF ×4
ADP ×4
Metals
_MG ×4
Waters ×409
* Residue conservation analysis
PDB id:
1rk2
Name: Transferase
Title: E. Coli ribokinase complexed with ribose and adp, solved in space group p212121
Structure: Ribokinase. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Cellular_location: cytoplasm. Gene: rbsk. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the rbsk gene was cloned behind aurce 11 trp-promoter, forming the plasmid pjgk10
Biol. unit: Tetramer (from PQS)
Resolution:
2.25Å     R-factor:   0.228     R-free:   0.265
Authors: J.A.Sigrell,A.D.Cameron,S.L.Mowbray
Key ref:
J.A.Sigrell et al. (1999). Induced fit on sugar binding activates ribokinase. J Mol Biol, 290, 1009-1018. PubMed id: 10438599 DOI: 10.1006/jmbi.1999.2938
Date:
20-May-99     Release date:   01-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A9J6  (RBSK_ECOLI) -  Ribokinase
Seq:
Struc:
309 a.a.
305 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.15  - Ribokinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate
ATP
+
D-ribose
Bound ligand (Het Group name = RIB)
corresponds exactly
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ D-ribose 5-phosphate
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   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2938 J Mol Biol 290:1009-1018 (1999)
PubMed id: 10438599  
 
 
Induced fit on sugar binding activates ribokinase.
J.A.Sigrell, A.D.Cameron, S.L.Mowbray.
 
  ABSTRACT  
 
The enzyme ribokinase phosphorylates ribose at O5* as the first step in its metabolism. The original X-ray structure of Escherichia coli ribokinase represented the ternary complex including ribose and ADP. Structures are presented here for the apo enzyme, as well as the ribose-bound state and four new ternary complex forms. Combined, the structures suggest that large and small conformational changes play critical roles in the function of this kinase. An initially open apo form can allow entry of the ribose substrate. After ribose binding, the active site lid is observed in a closed conformation, with the sugar trapped underneath. This closure and associated changes in the protein appear to assist ribokinase in recognition of the co-substrate ATP as the next step. Binding of the nucleotide brings about further, less dramatic adjustments in the enzyme structure. Additional small movements are almost certainly required during the phosphoryltransfer reaction. Evidence is presented that some types of movements of the lid are allowed in the ternary complex, which may be critical to the creation and breakdown of the transition state. Similar events are likely to take place during catalysis by other related carbohydrate kinases, including adenosine kinase.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Stereo plot of the original ternary complex (dark blue) and the most different lid conformation found among the new ternary complex structures (chain A, cyan). Ribose, ADP, phosphate and two nearby water molecules are shown; the phosphate molecule is absent in the latter structure. The apo protein is also shown (red). The struc- tural alignments were done using residues 116-192.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (1999, 290, 1009-1018) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19237742 C.H.Trinh, A.Asipu, D.T.Bonthron, and S.E.Phillips (2009).
Structures of alternatively spliced isoforms of human ketohexokinase.
  Acta Crystallogr D Biol Crystallogr, 65, 201-211.
PDB codes: 2hqq 2hw1
19548321 V.Guixé, and F.Merino (2009).
The ADP-dependent sugar kinase family: kinetic and evolutionary aspects.
  IUBMB Life, 61, 753-761.  
18625008 F.Merino, and V.Guixé (2008).
Specificity evolution of the ADP-dependent sugar kinase family: in silico studies of the glucokinase/phosphofructokinase bifunctional enzyme from Methanocaldococcus jannaschii.
  FEBS J, 275, 4033-4044.  
19021762 H.Ota, S.Sakasegawa, Y.Yasuda, S.Imamura, and T.Tamura (2008).
A novel nucleoside kinase from Burkholderia thailandensis.
  FEBS J, 275, 5865-5872.  
17597075 M.C.Reddy, S.K.Palaninathan, N.D.Shetty, J.L.Owen, M.D.Watson, and J.C.Sacchettini (2007).
High resolution crystal structures of Mycobacterium tuberculosis adenosine kinase: insights into the mechanism and specificity of this novel prokaryotic enzyme.
  J Biol Chem, 282, 27334-27342.
PDB codes: 2pkf 2pkk 2pkm 2pkn
17558452 P.O.Ogbunude, N.Lamour, and M.P.Barrett (2007).
Molecular cloning, expression and characterization of ribokinase of Leishmania major.
  Acta Biochim Biophys Sin (Shanghai), 39, 462-466.  
17242506 Y.Zhang, M.H.El Kouni, and S.E.Ealick (2007).
Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase.
  Acta Crystallogr D Biol Crystallogr, 63, 126-134.
PDB codes: 2a9y 2a9z 2aa0 2ab8
16929110 L.Arnfors, T.Hansen, P.Schönheit, R.Ladenstein, and W.Meining (2006).
Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
  Acta Crystallogr D Biol Crystallogr, 62, 1085-1097.
PDB codes: 2c49 2c4e
16519676 M.G.Tozzi, M.Camici, L.Mascia, F.Sgarrella, and P.L.Ipata (2006).
Pentose phosphates in nucleoside interconversion and catabolism.
  FEBS J, 273, 1089-1101.  
15590634 C.Wrenger, M.L.Eschbach, I.B.Müller, D.Warnecke, and R.D.Walter (2005).
Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasite Plasmodium falciparum.
  J Biol Chem, 280, 5242-5248.  
16030223 F.McArthur, C.E.Andersson, S.Loutet, S.L.Mowbray, and M.A.Valvano (2005).
Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis.
  J Bacteriol, 187, 5292-5300.  
15060078 K.S.Ryu, C.Kim, I.Kim, S.Yoo, B.S.Choi, and C.Park (2004).
NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration.
  J Biol Chem, 279, 25544-25548.  
14722069 M.H.Li, F.Kwok, W.R.Chang, S.Q.Liu, S.C.Lo, J.P.Zhang, T.Jiang, and D.C.Liang (2004).
Conformational changes in the reaction of pyridoxal kinase.
  J Biol Chem, 279, 17459-17465.
PDB codes: 1rft 1rfu 1rfv
12906824 N.Manoj, E.Strauss, T.P.Begley, and S.E.Ealick (2003).
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
  Structure, 11, 927-936.
PDB code: 1p9o
12527754 R.Cabrera, H.Fischer, S.Trapani, A.F.Craievich, R.C.Garratt, V.Guixé, and J.Babul (2003).
Domain motions and quaternary packing of phosphofructokinase-2 from Escherichia coli studied by small angle x-ray scattering and homology modeling.
  J Biol Chem, 278, 12913-12919.  
12237466 H.Tsuge, H.Sakuraba, T.Kobe, A.Kujime, N.Katunuma, and T.Ohshima (2002).
Crystal structure of the ADP-dependent glucokinase from Pyrococcus horikoshii at 2.0-A resolution: a large conformational change in ADP-dependent glucokinase.
  Protein Sci, 11, 2456-2463.
PDB code: 1l2l
11900549 M.C.Maj, B.Singh, and R.S.Gupta (2002).
Pentavalent ions dependency is a conserved property of adenosine kinase from diverse sources: identification of a novel motif implicated in phosphate and magnesium ion binding and substrate inhibition.
  Biochemistry, 41, 4059-4069.  
12235162 M.H.Li, F.Kwok, W.R.Chang, C.K.Lau, J.P.Zhang, S.C.Lo, T.Jiang, and D.C.Liang (2002).
Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
  J Biol Chem, 277, 46385-46390.
PDB codes: 1lhp 1lhr
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.