PDBsum entry 1r0l

Oxidoreductase

PDB id: 1r0l

Contents

Protein chains

378 a.a. *

Ligands

NDP ×4

Waters ×108

* Residue conservation analysis

PDB id:

1r0l

Name:

Oxidoreductase

Title:

1-deoxy-d-xylulose 5-phosphate reductoisomerase from zymomonas mobilis in complex with NADPH

Structure:

1-deoxy-d-xylulose 5-phosphate reductoisomerase. Chain: a, b, c, d. Synonym: dxp reductoisomerase, 1-deoxyxylulose-5-phosphate reductoisomerase. Engineered: yes

Source:

Zymomonas mobilis. Organism_taxid: 542. Gene: dxr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.249 R-free: 0.269

Authors:

S.Ricagno,S.Grolle,S.Bringer-Meyer,H.Sahm,Y.Lindqvist,G.Schneider

Key ref:

S.Ricagno et al. (2004). Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase from Zymomonas mobilis at 1.9-A resolution. Biochim Biophys Acta, 1698, 37-44. PubMed id: 15063313 DOI: 10.1016/j.bbapap.2003.10.006

Date:

22-Sep-03 Release date: 13-Jul-04

Protein chains

Q9X5F2  (DXR_ZYMMO) -  1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)

Seq: 388 a.a.

Struc: 378 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.267 - 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
• Reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP⁺ = 1-deoxy-D-xylulose 5-phosphate + NADPH + H⁺

2-C-methyl-D-erythritol 4-phosphate + NADP(+) (Bound ligand (Het Group name = NDP) matches with 56.25% similarity) = 1-deoxy-D-xylulose 5-phosphate + NADPH + H(+)

• Cofactor: Mg(2+) or cobalt cation or Mn(2+)

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

reference

DOI no: 10.1016/j.bbapap.2003.10.006

Biochim Biophys Acta 1698:37-44 (2004)

PubMed id: 15063313

Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase from Zymomonas mobilis at 1.9-A resolution.

S.Ricagno, S.Grolle, S.Bringer-Meyer, H.Sahm, Y.Lindqvist, G.Schneider.

ABSTRACT

1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) is the second enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. The structure of the apo-form of this enzyme from Zymomonas mobilis has been solved and refined to 1.9-A resolution, and that of a binary complex with the co-substrate NADPH to 2.7-A resolution. The subunit of DXR consists of three domains. Residues 1-150 form the NADPH binding domain, which is a variant of the typical dinucleotide-binding fold. The second domain comprises a four-stranded mixed beta-sheet, with three helices flanking the sheet. Most of the putative active site residues are located on this domain. The C-terminal domain (residues 300-386) folds into a four-helix bundle. In solution and in the crystal, the enzyme forms a homo-dimer. The interface between the two monomers is formed predominantly by extension of the sheet in the second domain. The adenosine phosphate moiety of NADPH binds to the nucleotide-binding fold in the canonical way. The adenine ring interacts with the loop after beta1 and with the loops between alpha2 and beta2 and alpha5 and beta5. The nicotinamide ring is disordered in crystals of this binary complex. Comparisons to Escherichia coli DXR show that the two enzymes are very similar in structure, and that the active site architecture is highly conserved. However, there are differences in the recognition of the adenine ring of NADPH in the two enzymes.