PDBsum entry: 1eq0

Transferase

PDB id: 1eq0

Contents

Protein chain

158 a.a. *

* Residue conservation analysis

PDB id:

1eq0

Name:

Transferase

Title:

Solution structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with mgamppcp

Structure:

6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Chain: a. Synonym: hppk. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

G.Shi,H.Yan

Key ref:

B.Xiao et al. (2001). Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR. J Biol Chem, 276, 40274-40281. PubMed id: 11546767 Ref: Full text

Date:

30-Mar-00 Release date: 07-Nov-01

Protein chain

P26281  (HPPK_ECOLI) -  2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

Seq: 159 a.a.

Struc: 158 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.6.3 - 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.
• Pathway: Folate Biosynthesis (late stages)
• Reaction: ATP + 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine = AMP + (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: folic acid and derivative biosynthetic process (2 terms)
• Biochemical function: nucleotide binding (5 terms)

reference

Full text	J Biol Chem 276:40274-40281 (2001)
PubMed id: 11546767

Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR.

B.Xiao, G.Shi, J.Gao, J.Blaszczyk, Q.Liu, X.Ji, H.Yan.

ABSTRACT

The crystal structure of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in complex with MgADP has been determined at 1.5-A resolution with a crystallographic R factor of 0.191. The solution structure of HPPK in complex with Mg(2+) and beta,gamma-methyleneadenosine 5'-triphosphate (MgAMPPCP) has been determined using a simulated annealing protocol with 3,523 experimental NMR restraints. The root mean square deviation of the ensemble of 20 refined conformers that represent the solution structure from the mean coordinate set derived from them is 0.74 +/- 0.26 A for all backbone atoms and 0.49 +/- 0.22 A when residues Pro(14), Pro(44)-Gln(50), and Arg(84)-Pro(91) are excluded. Binding of MgADP causes significant changes in the conformation and dynamical property of three loops of HPPK that are involved in catalysis. A dramatic, unusual conformational change is that loop 3 moves away from the active center significantly with some residues moving by >17 A. The binding of MgADP also stabilizes loop 1 and loop 3 but makes loop 2 more mobile. Very similar conformational and dynamical changes are observed in the NMR solution structure of HPPK.MgAMPPCP. The conformational and dynamical changes may play important roles in both substrate binding and product release in the catalytic cycle.

Selected figure(s)

Figure 2.
Fig. 2. Stereo view of MgADP-protein interactions. a and b illustrate the interactions of protein with two distinct conformations of ADP. The models are illustrated as ball-and-sticks with filled bonds for protein and open bonds for ADP. Dashed lines represent electrostatic interactions. Atomic color is used with carbon in black, nitrogen in blue, oxygen in red, magnesium in green, and phosphorus in pink. The figure was made with the program Molscript (22).

Figure 8.
Fig. 8. Induced fit in HPPK from apo-HPPK (green) to HPPK·HP·MgAMPCPP (yellow) (a) and from apo-HPPK (green) to HPPK·MgADP (yellow) (b). In panel a, the side chains of apo-HPPK are shown in green and those of HPPK·HP·MgAMPCPP in gray; the two Mg2+ ions are in cyan. In panel b, the side chains of apo-HPPK are shown in green and those of HPPK·MgADP in gray; the Mg2+ ion of HPPK·MgADP is in cyan (Mg1); and the side chains of Asp95 and the two Mg2+ ions (Mg2 and Mg3) of HPPK·HP·MgAMPCPP are in orange. The figure was made with the program Molscript (22) and Raster3D (23, 24).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 40274-40281) copyright 2001.

Figures were selected by an automated process.