PDBsum entry 1v9a

Transferase

PDB id: 1v9a

Contents

Protein chains

219 a.a. *

Ligands

FLC ×2

SAH ×2

Waters ×209

* Residue conservation analysis

PDB id:

1v9a

Name:

Transferase

Title:

Crystal structure of uroporphyrin-iii c-methyl transferase from thermus thermophilus complexed with s-adenyl homocysteine

Structure:

Uroporphyrin-iii c-methyltransferase. Chain: a, b. Synonym: hypothetical protein ttha0667. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.215 R-free: 0.246

Authors:

P.H.Rehse,T.Kitao,T.H.Tahirov,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

P.H.Rehse et al. (2005). Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr, 61, 913-919. PubMed id: 15983414 DOI: 10.1107/S0907444905008838

Date:

23-Jan-04 Release date: 01-Feb-05

Protein chains

Q5SKH6  (Q5SKH6_THET8) -  uroporphyrinogen-III C-methyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 240 a.a.

Struc: 219 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.107 - uroporphyrinogen-III C-methyltransferase.
• Pathway: Corrin Biosynthesis (part 1)
• Reaction: uroporphyrinogen III + 2 S-adenosyl-L-methionine = precorrin-2 + 2 S-adenosyl-L-homocysteine + H⁺

uroporphyrinogen III + 2 × S-adenosyl-L-methionine = precorrin-2 + 2 × 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: 10.1107/S0907444905008838

Acta Crystallogr D Biol Crystallogr 61:913-919 (2005)

PubMed id: 15983414

Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus.

P.H.Rehse, T.Kitao, T.H.Tahirov.

ABSTRACT

Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a multifunctional protein responsible for two of the eight S-adenosyl-methionine-dependent methylations of the corrin ring during vitamin B(12) synthesis. The structure of this protein has been solved to 2.0 A resolution in both the apo and cofactor-bound form. The monomer consists of two domains, A and B, each consisting of a five-stranded beta-sheet and two or three alpha-helices, with the cofactor bound at the interface. The biological unit is the dimer found in the asymmetric unit. This dimer is related by a non-crystallographic twofold such that two B domains combine to form a long ten-stranded beta-sheet. When compared with solved related structures, this structure shows clear differences in the region involved in cofactor and substrate binding, affirming the role of several previously implicated residues and questioning others. The solved related structures are characterized by an exposed active site. The T. thermophilus structure has this site restricted by the interaction of a flexible loop structure with a highly conserved residue, suggesting a mechanistic role. This structure represents the ;closed' form of the protein.

Selected figure(s)

Figure 1.
Figure 1 Structure of precorrin-2, the product of SAM-dependent uroporphyrinogen-III C-methyltransferase. The two independent methylation sites are designated 1 and 2. Methylation only at site 1 generates the intermediate precorrin-1.

Figure 4.
Figure 4 Stereo diagram of the cofactor-binding site of uroporphyrinogen-III C-methyltransferase from T. thermophilus (ttSUMT).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 913-919) copyright 2005.

Figures were selected by an automated process.