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PDBsum entry 2i5b

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2i5b
Jmol
Contents
Protein chains
269 a.a. *
Ligands
ADP ×5
* Residue conservation analysis
PDB id:
2i5b
Name: Transferase
Title: The crystal structure of an adp complex of bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution
Structure: Phosphomethylpyrimidine kinase. Chain: a, c, d, b, e. Synonym: hmp-phosphate kinase, hmp-p kinase. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Strain: 168. Gene: thid. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
Resolution:
2.80Å     R-factor:   0.225     R-free:   0.274
Authors: J.A.Newman,S.K.Das,S.E.Sedelnikova,D.W.Rice
Key ref:
J.A.Newman et al. (2006). The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution. J Mol Biol, 363, 520-530. PubMed id: 16978644 DOI: 10.1016/j.jmb.2006.08.013
Date:
24-Aug-06     Release date:   19-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P39610  (PDXK_BACSU) -  Pyridoxine kinase
Seq:
Struc:
271 a.a.
269 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.35  - Pyridoxal kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
ATP
+ pyridoxal
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   2 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.08.013 J Mol Biol 363:520-530 (2006)
PubMed id: 16978644  
 
 
The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
J.A.Newman, S.K.Das, S.E.Sedelnikova, D.W.Rice.
 
  ABSTRACT  
 
Pyridoxal kinase catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal 5' phosphate salvage pathway. The crystal structure of a dimeric pyridoxal kinase from Bacillus subtilis has been solved in complex with ADP to 2.8 A resolution. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other ribokinase superfamily members reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal kinases, suggesting that this structure represents the first for a novel family of "HMPP kinase-like" pyridoxal kinases. Moreover this further suggests that this enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Stereo view of B. subtilis PdxK, with the elements of secondary structure shown in cartoon representation and labelled according to PdxK nomenclature. α-Helices are in red, β-strands in yellow, loops in green and the ADP molecule is shown in stick format. (b) PdxK dimer viewed with the 2-fold axis vertical. (c) Representation of the residues involved in forming the dimer interface shown in stick representation and contacting the surface of a 2-fold related partner. The interface lies away from the active site and is highly complementary in shape and accounts for 16% of the total accessible surface area of each subunit. Figure 1. (a) Stereo view of B. subtilis PdxK, with the elements of secondary structure shown in cartoon representation and labelled according to PdxK nomenclature. α-Helices are in red, β-strands in yellow, loops in green and the ADP molecule is shown in stick format. (b) PdxK dimer viewed with the 2-fold axis vertical. (c) Representation of the residues involved in forming the dimer interface shown in stick representation and contacting the surface of a 2-fold related partner. The interface lies away from the active site and is highly complementary in shape and accounts for 16% of the total accessible surface area of each subunit. This and all subsequent figures in this paper (with the exception of [3]Figure 5) were generated using PyMOL.[4]^46
Figure 4.
Figure 4. Stereo diagram of a comparison between the B. subtilis PdxK substrate-binding site (red throughout) with (a) sheep brain pyridoxal kinase (brown) and E.coli PdxY (dark blue), (b) S. typhimurium HMPP kinase (green) and T. thermophilus HMPP kinase (orange). The substrate pyridoxal is shown in its expected position throughout in the ball and stick representation (light blue). Figure 4. Stereo diagram of a comparison between the B. subtilis PdxK substrate-binding site (red throughout) with (a) sheep brain pyridoxal kinase (brown) and E.coli PdxY (dark blue), (b) S. typhimurium HMPP kinase (green) and T. thermophilus HMPP kinase (orange). The substrate pyridoxal is shown in its expected position throughout in the ball and stick representation (light blue).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 363, 520-530) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17766369 F.N.Musayev, M.L.di Salvo, T.P.Ko, A.K.Gandhi, A.Goswami, V.Schirch, and M.K.Safo (2007).
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
  Protein Sci, 16, 2184-2194.
PDB codes: 2yxt 2yxu
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