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PDBsum entry 1h3m

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1h3m
Jmol
Contents
Protein chains
215 a.a. *
Ligands
N2P
Metals
_CL ×5
Waters ×86
* Residue conservation analysis
PDB id:
1h3m
Name: Transferase
Title: Structure of 4-diphosphocytidyl-2c-methyl-d-erythritol synthetase
Structure: 2-c-methyl-d-erythritol 4-phosphate cytidylyltransferase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3). Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.4Å     R-factor:   0.241     R-free:   0.333
Authors: L.E.Kemp,C.S.Bond,W.N.Hunter
Key ref:
L.E.Kemp et al. (2003). Structure of a tetragonal crystal form of Escherichia coli 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase. Acta Crystallogr D Biol Crystallogr, 59, 607-610. PubMed id: 12595740 DOI: 10.1107/S090744490202365X
Date:
10-Sep-02     Release date:   01-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q46893  (ISPD_ECOLI) -  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Seq:
Struc:
236 a.a.
215 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     isoprenoid biosynthetic process   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1107/S090744490202365X Acta Crystallogr D Biol Crystallogr 59:607-610 (2003)
PubMed id: 12595740  
 
 
Structure of a tetragonal crystal form of Escherichia coli 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
L.E.Kemp, C.S.Bond, W.N.Hunter.
 
  ABSTRACT  
 
2-C-Methyl-D-erythritol 4-phosphate cytidylyltransferase is an essential enzyme in the mevalonate-independent pathway of isoprenoid biosynthesis. The structure of a tetragonal crystal form has been solved by molecular replacement and refined to 2.4 A resolution. Structure and sequence comparisons suggest that the enzyme is a suitable target for a structure-based approach to the development of novel broad-spectrum antibiotics. However, the absence of ligands in the enzyme active site together with the moderate resolution of the structure indicates that this tetragonal crystal form is inferior to that of a previously reported highly ordered monoclinic form [Richard et al. (2001), Nature Struct. Biol. 8, 641-647].
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Stereoview C^ trace of the MEPC dimer (subunit A, cyan; subunit B, black). One active site (subunit B) is labelled and the C^ positions of strictly conserved residues around this active site are depicted as red spheres. Every 20th C^ position starting from residue 10, with the exception of residue 190B, is depicted as a black sphere and numbered in black for subunit A and in blue for subunit B. Residue Asp190B is strictly conserved in MEPC and is depicted with a red sphere at the active site.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 607-610) copyright 2003.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22522421 T.Roscioli, E.J.Kamsteeg, K.Buysse, I.Maystadt, J.van Reeuwijk, C.van den Elzen, E.van Beusekom, M.Riemersma, R.Pfundt, L.E.Vissers, M.Schraders, U.Altunoglu, M.F.Buckley, H.G.Brunner, B.Grisart, H.Zhou, J.A.Veltman, C.Gilissen, G.M.Mancini, P.Delrée, M.A.Willemsen, D.P.Ramadža, D.Chitayat, C.Bennett, E.Sheridan, E.A.Peeters, G.M.Tan-Sindhunata, C.E.de Die-Smulders, K.Devriendt, H.Kayserili, O.A.El-Hashash, D.L.Stemple, D.J.Lefeber, Y.Y.Lin, and H.van Bokhoven (2012).
Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of α-dystroglycan.
  Nat Genet, 44, 581-585.  
21543842 C.Björkelid, T.Bergfors, L.M.Henriksson, A.L.Stern, T.Unge, S.L.Mowbray, and T.A.Jones (2011).
Structural and functional studies of mycobacterial IspD enzymes.
  Acta Crystallogr D Biol Crystallogr, 67, 403-414.
PDB codes: 2xwl 2xwm 2xwn
19074383 S.Baur, J.Marles-Wright, S.Buckenmaier, R.J.Lewis, and W.Vollmer (2009).
Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae.
  J Bacteriol, 191, 1200-1210.
PDB codes: 2vsh 2vsi
17442674 W.N.Hunter (2007).
The non-mevalonate pathway of isoprenoid precursor biosynthesis.
  J Biol Chem, 282, 21573-21577.  
16478479 M.Gabrielsen, J.Kaiser, F.Rohdich, W.Eisenreich, R.Laupitz, A.Bacher, C.S.Bond, and W.N.Hunter (2006).
The crystal structure of a plant 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphate.
  FEBS J, 273, 1065-1073.
PDB code: 1w77
15466439 M.Gabrielsen, C.S.Bond, I.Hallyburton, S.Hecht, A.Bacher, W.Eisenreich, F.Rohdich, and W.N.Hunter (2004).
Hexameric assembly of the bifunctional methylerythritol 2,4-cyclodiphosphate synthase and protein-protein associations in the deoxy-xylulose-dependent pathway of isoprenoid precursor biosynthesis.
  J Biol Chem, 279, 52753-52761.
PDB codes: 1w55 1w57
15233799 M.Gabrielsen, F.Rohdich, W.Eisenreich, T.Gräwert, S.Hecht, A.Bacher, and W.N.Hunter (2004).
Biosynthesis of isoprenoids: a bifunctional IspDF enzyme from Campylobacter jejuni.
  Eur J Biochem, 271, 3028-3035.  
12878729 L.Miallau, M.S.Alphey, L.E.Kemp, G.A.Leonard, S.M.McSweeney, S.Hecht, A.Bacher, W.Eisenreich, F.Rohdich, and W.N.Hunter (2003).
Biosynthesis of isoprenoids: crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol kinase.
  Proc Natl Acad Sci U S A, 100, 9173-9178.
PDB code: 1oj4
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