PDBsum entry 2plm

Unknown function

PDB id: 2plm

Contents

Protein chain

404 a.a. *

Ligands

SIB

Metals

_ZN

Waters ×74

* Residue conservation analysis

PDB id:

2plm

Name:

Unknown function

Title:

Crystal structure of the protein tm0936 from thermotoga maritima complexed with zn and s-inosylhomocysteine

Structure:

Uncharacterized protein. Chain: a. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.209 R-free: 0.238

Authors:

A.A.Fedorov,E.V.Fedorov,J.C.Hermann,R.Marti-Arbona,B.K.Shoichet, F.M.Raushel,S.C.Almo

Key ref:

J.C.Hermann et al. (2007). Structure-based activity prediction for an enzyme of unknown function. Nature, 448, 775-779. PubMed id: 17603473 DOI: 10.1038/nature05981

Date:

20-Apr-07 Release date: 17-Jul-07

Protein chain

Q9X034  (MTAD_THEMA) -  5-methylthioadenosine/S-adenosylhomocysteine deaminase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 406 a.a.

Struc: 404 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.5.4.28 - S-adenosylhomocysteine deaminase.
• Reaction: S-adenosyl-L-homocysteine + H2O + H⁺ = S-inosyl-L-homocysteine + NH4⁺

S-adenosyl-L-homocysteine + H2O + H(+) = S-inosyl-L-homocysteine + NH4(+) (Bound ligand (Het Group name = SIB) corresponds exactly)

• Enzyme class 2: E.C.3.5.4.31 - S-methyl-5'-thioadenosine deaminase.
• Reaction: S-methyl-5'-thioadenosine + H2O + H⁺ = S-methyl-5'-thioinosine + NH4⁺

S-methyl-5'-thioadenosine + H2O + H(+) (Bound ligand (Het Group name = SIB) matches with 70.37% similarity) = S-methyl-5'-thioinosine + NH4(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nature05981

Nature 448:775-779 (2007)

PubMed id: 17603473

Structure-based activity prediction for an enzyme of unknown function.

J.C.Hermann, R.Marti-Arbona, A.A.Fedorov, E.Fedorov, S.C.Almo, B.K.Shoichet, F.M.Raushel.

ABSTRACT

With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10(5) M(-1 )s(-1)). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.

Selected figure(s)

Figure 1.
Figure 1: Sample transformations of metabolites from their ground state structure into the high-energy intermediate forms that were used for docking. Transformations were computed according to the conserved reaction mechanism of amidohydrolases, a nucleophilic attack of a hydroxide at an electrophilic centre atom. Every transformable functional group for each molecule was processed independently. If the high-energy structure was chiral, all stereoisomers were calculated. Reactions catalysed by the amidohydrolases cytosine deaminase (CDA), adenosine deaminase (ADA), dihydroorotase (DHO), D-hydantoinase (HYD), isoaspartyl-d-dipeptidase (IAD), N-acetyl-D-glucosamine-6-phosphate deacetylase (NaGA) and phosphotriesterase (PTE) are shown.

Figure 3.
Figure 3: Comparing the docking prediction and the crystallographic result.
Figure 3 : Comparing the docking prediction and the crystallographic result.
Superposition of the crystal structure of Tm0936 in complex with SIH (red) and the docking predicted structure of the high-energy intermediate of SAH (carbons in green). Enzyme carbons are coloured light blue, SAH and enzyme oxygen atoms are coloured red, nitrogens blue and sulphurs orange. The purple sphere represents the divalent metal ion. An F[O] – F[C] omit electron density map for SIH is shown, contoured at 4.1 . The structure was determined at 2.1 Å resolution.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 448, 775-779) copyright 2007.

Figures were selected by an automated process.