PDBsum entry 1x1c

Transferase

PDB id: 1x1c

Contents

Protein chain

337 a.a. *

Ligands

SO4

SAH

GOL

Metals

_ZN ×5

Waters ×20

* Residue conservation analysis

PDB id:

1x1c

Name:

Transferase

Title:

Crystal structure of bchu complexed with s-adenosyl-l-homocysteine and zn2+

Structure:

Crtf-related protein. Chain: a. Synonym: methyltransferase. Engineered: yes

Source:

Chlorobium tepidum. Organism_taxid: 194439. Strain: tls. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.85Å R-factor: 0.230 R-free: 0.288

Authors:

H.Yamaguchi,K.Wada,K.Fukuyama

Key ref:

K.Wada et al. (2006). Crystal structures of BchU, a methyltransferase involved in bacteriochlorophyll c biosynthesis, and its complex with S-adenosylhomocysteine: implications for reaction mechanism. J Mol Biol, 360, 839-849. PubMed id: 16797589 DOI: 10.1016/j.jmb.2006.05.057

Date:

03-Apr-05 Release date: 18-Jul-06

Protein chain

Q8KGE0  (Q8KGE0_CHLTE) -  Bacteriochlorophyllide d C-20 methyltransferase from Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)

Seq: 338 a.a.

Struc: 337 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.333 - bacteriochlorophyllide d C-20 methyltransferase.
• Reaction: a bacteriochlorophyllide d + S-adenosyl-L-methionine = a bacteriochlorophyllide c + S-adenosyl-L-homocysteine + H⁺

bacteriochlorophyllide d + S-adenosyl-L-methionine = bacteriochlorophyllide c + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

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

reference

DOI no: 10.1016/j.jmb.2006.05.057

J Mol Biol 360:839-849 (2006)

PubMed id: 16797589

Crystal structures of BchU, a methyltransferase involved in bacteriochlorophyll c biosynthesis, and its complex with S-adenosylhomocysteine: implications for reaction mechanism.

K.Wada, H.Yamaguchi, J.Harada, K.Niimi, S.Osumi, Y.Saga, H.Oh-Oka, H.Tamiaki, K.Fukuyama.

ABSTRACT

BchU plays a role in bacteriochlorophyll c biosynthesis by catalyzing methylation at the C-20 position of cyclic tetrapyrrole chlorin using S-adenosylmethionine (SAM) as a methyl source. This methylation causes red-shifts of the electronic absorption spectrum of the light-harvesting pigment, allowing green photosynthetic bacteria to adapt to low-light environments. We have determined the crystal structures of BchU and its complex with S-adenosylhomocysteine (SAH). BchU forms a dimer and each subunit consists of two domains, an N-terminal domain and a C-terminal domain. Dimerization occurs through interactions between the N-terminal domains and the residues responsible for the catalytic reaction are in the C-terminal domain. The binding site of SAH is located in a large cavity between the two domains, where SAH is specifically recognized by many hydrogen bonds and a salt-bridge. The electron density map of BchU in complex with an analog of bacteriochlorophyll c located its central metal near the SAH-binding site, but the tetrapyrrole ring was invisible, suggesting that binding of the ring to BchU is loose and/or occupancy of the ring is low. It is likely that His290 acts as a ligand for the central metal of the substrate. The orientation of the substrate was predicted by simulation, and allows us to propose a mechanism for the BchU directed methylation: the strictly conserved Tyr246 residue acts catalytically in the direct transfer of the methyl group from SAM to the substrate through an S(N)2-like mechanism.

Selected figure(s)

Figure 1.
Figure 1. Methylation catalyzed by Chl. tepidum BchU. Compounds: 1, 8-ethyl-12-methyl-bacteriochlorophyllide d; 2, 8-ethyl-12-methyl-bacteriochlorophyllide c.

Figure 9.
Figure 9. A proposed reaction mechanism for C-20 methylation of Zn BChlid d to Zn-BChlid c by SAM and BchU.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 839-849) copyright 2006.

Figures were selected by an automated process.