PDBsum entry 2asf

Structural genomics, unknown function

PDB id: 2asf

Contents

Protein chain

125 a.a. *

Ligands

CIT ×2

Metals

_NA

Waters ×175

* Residue conservation analysis

PDB id:

2asf

Name:

Structural genomics, unknown function

Title:

Crystal structure of the conserved hypothetical protein rv2074 from mycobacterium tuberculosis 1.6 a

Structure:

Hypothetical protein rv2074. Chain: a. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

1.60Å R-factor: 0.180 R-free: 0.204

Authors:

B.K.Biswal,K.Au,M.M.Cherney,C.Garen,M.N.James,Tb Structural Genomics Consortium (Tbsgc)

Key ref:

B.K.Biswal et al. (2006). The molecular structure of Rv2074, a probable pyridoxine 5'-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 angstroms resolution. Acta Crystallograph Sect F Struct Biol Cryst Commun, 62, 735-742. PubMed id: 16880544 DOI: 10.1107/S1744309106025012

Date:

23-Aug-05 Release date: 11-Oct-05

Protein chain

P9WLL7  (FBVR_MYCTU) -  F420H(2)-dependent biliverdin reductase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 137 a.a.

Struc: 125 a.a.

Enzyme reactions

• Enzyme class: E.C.1.3.98.- - ?????

DOI no: 10.1107/S1744309106025012

Acta Crystallograph Sect F Struct Biol Cryst Commun 62:735-742 (2006)

PubMed id: 16880544

The molecular structure of Rv2074, a probable pyridoxine 5'-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 angstroms resolution.

B.K.Biswal, K.Au, M.M.Cherney, C.Garen, M.N.James.

ABSTRACT

The crystal structure of a conserved hypothetical protein corresponding to open reading frame Rv2074 from Mycobacterium tuberculosis (Mtb) has been solved by the two-wavelength anomalous dispersion method. Refinement of the molecular structure at 1.6 angstroms resolution resulted in an R(work) of 0.178 and an R(free) of 0.204. The crystal asymmetric unit contains an Rv2074 monomer; however, the crystallographic twofold symmetry operation of space group P4(3)2(1)2 generates dimeric Rv2074. Each monomer folds into a six-stranded antiparallel beta-barrel flanked by two alpha-helices. The three-dimensional structure of Rv2074 is very similar to that of Mtb Rv1155, a probable pyridoxine 5'-phosphate oxidase (PNPOx), which corroborates well with the relatively high sequence similarity (52%) between the two. A structural comparison between Rv2074 and Rv1155 revealed that the core structure (a six-stranded beta-barrel) is also well conserved; the major differences between the two lie in the N- and C-termini and in the small helical domain. Two citric acid molecules were observed in the active site of Rv2074, the crystals of which were grown in 0.2 M sodium citrate buffer pH 5.0. The citric acid molecules are bound to Rv2074 by hydrogen-bonding interactions with Thr55, Gln60 and Lys61. One of the two citric acid molecules occupies the same spatial position that corresponds to the position of the phosphate and ribose sugar moieties of the flavin mononucleotide (FMN) in the Mtb Rv1155-FMN, Escherichia coli PNPOx-FMN and human PNPOx-FMN complex structures. Owing to its extensive structural similarity with Mtb Rv1155 and to the E. coli and human PNPOx enzymes, Rv2074 may be involved in the final step in the biosynthesis of pyridoxal 5'-phosphate (PLP; a vitamin B6).

Selected figure(s)

Figure 2.
Figure 2 Stereoview of the six-stranded antiparallel -barrel structure of Rv2074. This figure and Figs. 5-and 6-were prepared using the program PyMOL (http://pymol.sourceforge.net ).

Figure 7.
Figure 7 (a) Stereoview of the 2|F[o]| - |F[c]| electron-density map (blue) contoured at the 1 level, showing two citric acid molecules bound in the active site of Rv2074. The citrate C and O atoms are shown in grey and red, respectively. Also shown are the Na atom and coordinating water molecules. This figure was prepared by the program BOBSCRIPT (Esnouf, 1999[Esnouf, R. M. (1999). Acta Cryst. D55, 938-940.]). (b) Stereoview of the interactions between the citric acid molecules and Rv2074. The C atoms of citric acid molecules and Rv2074 are shown in grey and cyan, respectively. Hydrogen and coordination bonds are shown in green and black, respectively.

The above figures are reprinted by permission from the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2006, 62, 735-742) copyright 2006.

Figures were selected by the author.