PDBsum entry 1s4d

Transferase

PDB id: 1s4d

Contents

Protein chains

(+ 6 more) 256 a.a. *

Ligands

SAH ×12

GOL ×26

Waters ×523

* Residue conservation analysis

PDB id:

1s4d

Name:

Transferase

Title:

Crystal structure analysis of the s-adenosyl-l-methionine dependent uroporphyrinogen-iii c-methyltransferase sumt

Structure:

Uroporphyrin-iii c-methyltransferase. Chain: a, b, d, e, f, g, h, i, j, k, l, m. Synonym: s-adenosyl-l-methionine uroporphyrinogen-iii c- methyltransferase, urogen iii methylase, sumt, uroporphyrinogen iii methylase, urom. Engineered: yes

Source:

Pseudomonas denitrificans. Organism_taxid: 43306. Gene: coba. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.215 R-free: 0.260

Authors:

J.Vevodova,R.M.Graham,E.Raux,H.L.Schubert,D.I.Roper,A.A.Brindley, A.I.Scott,C.A.Roessner,N.P.J.Stamford,M.E.Stroupe,E.D.Getzoff, M.J.Warren,K.S.Wilson

Key ref:

J.Vévodová et al. (2004). Structure/function studies on a S-adenosyl-L-methionine-dependent uroporphyrinogen III C methyltransferase (SUMT), a key regulatory enzyme of tetrapyrrole biosynthesis. J Mol Biol, 344, 419-433. PubMed id: 15522295 DOI: 10.1016/j.jmb.2004.09.020

Date:

16-Jan-04 Release date: 30-Nov-04

Protein chains

P21631  (SUMT_SINSX) -  Uroporphyrinogen-III C-methyltransferase from Sinorhizobium sp

Seq: 280 a.a.

Struc: 256 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: 10.1016/j.jmb.2004.09.020

J Mol Biol 344:419-433 (2004)

PubMed id: 15522295

Structure/function studies on a S-adenosyl-L-methionine-dependent uroporphyrinogen III C methyltransferase (SUMT), a key regulatory enzyme of tetrapyrrole biosynthesis.

J.Vévodová, R.M.Graham, E.Raux, H.L.Schubert, D.I.Roper, A.A.Brindley, A.Ian Scott, C.A.Roessner, N.P.Stamford, M.Elizabeth Stroupe, E.D.Getzoff, M.J.Warren, K.S.Wilson.

ABSTRACT

The crystallographic structure of the Pseudomonas denitrificans S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase (SUMT), which is encoded by the cobA gene, has been solved by molecular replacement to 2.7A resolution. SUMT is a branchpoint enzyme that plays a key role in the biosynthesis of modified tetrapyrroles by controlling flux to compounds such as vitamin B(12) and sirohaem, and catalysing the transformation of uroporphyrinogen III into precorrin-2. The overall topology of the enzyme is similar to that of the SUMT module of sirohaem synthase (CysG) and the cobalt-precorrin-4 methyltransferase CbiF and, as with the latter structures, SUMT has the product S-adenosyl-L-homocysteine bound in the crystal. The roles of a number of residues within the SUMT structure are discussed with respect to their conservation either across the broader family of cobalamin biosynthetic methyltransferases or within the sub-group of SUMT members. The D47N, L49A, F106A, T130A, Y183A and M184A variants of SUMT were generated by mutagenesis of the cobA gene, and tested for SAM binding and enzymatic activity. Of these variants, only D47N and L49A bound the co-substrate S-adenosyl-L-methionine. Consequently, all the mutants were severely restricted in their capacity to synthesise precorrin-2, although both the D47N and L49A variants produced significant quantities of precorrin-1, the monomethylated derivative of uroporphyrinogen III. The activity of these variants is interpreted with respect to the structure of the enzyme.

Selected figure(s)

Figure 4.
Figure 4. (a) Structure-based alignment of the sequences of the transmethylase enzymes and domains from P. denitrificans SUMT, Salmonella enterica CysG (multifunctional sirohaem synthase) and Bacillus megaterium CbiF (anaerobic cobalt-precorrin-4 methyltransferase) with the secondary structure labelled. The 3D alignment was performed using the SSM protein structure matching web page (http://www.ebi.ac.uk/msd-srv/ssm). The residues indicated with cyan dotted lines are either not modelled in the electron density or excluded from the alignment by SSM as being too far apart to be considered equivalent. (b) Superposition of the SUMT, CysG and CbiF molecules including SAH. The position of the ligand is almost identical in the three molecules. SUMT is coloured cyan, CysG magenta and CbiF yellow (all including their ligands).

Figure 5.
Figure 5. (a) SAH binding by surrounding (2.6-3.8 Å) residues is shown. Residues highlighted in the Figure interact directly with SAH either by H-bonds or by van der Waals contacts. (b) Molecule of SAH. 1s electron density from a 2F[o] -F[c] map contoured in blue.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 344, 419-433) copyright 2004.

Figures were selected by an automated process.