PDBsum entry 3iwc

Lyase

PDB id: 3iwc

Contents

Protein chains

61 a.a. *

59 a.a. *

56 a.a. *

Ligands

SMM ×2

Waters ×108

* Residue conservation analysis

PDB id:

3iwc

Name:

Lyase

Title:

T. Maritima adometdc complex with s-adenosylmethionine methyl ester

Structure:

S-adenosylmethionine decarboxylase. Chain: b, d. Fragment: residues 1-62. Synonym: adometdc, samdc, s-adenosylmethionine decarboxylase beta chain, s-adenosylmethionine decarboxylase alpha chain. Engineered: yes. S-adenosylmethionine decarboxylase. Chain: a, c. Fragment: residues 64-130.

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: speh, tm_0655. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.212 R-free: 0.238

Authors:

S.Bale,B.Kavita,S.E.Ealick

Key ref:

S.Bale et al. (2010). Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity. Acta Crystallogr D Biol Crystallogr, 66, 181-189. PubMed id: 20124698 DOI: 10.1107/S090744490904877X

Date:

02-Sep-09 Release date: 09-Feb-10

Protein chains

Q9WZC3  (SPEH_THEMA) -  S-adenosylmethionine decarboxylase proenzyme from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 130 a.a.

Struc: 61 a.a.

Protein chain

Q9WZC3  (SPEH_THEMA) -  S-adenosylmethionine decarboxylase proenzyme from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 130 a.a.

Struc: 59 a.a.*

Protein chain

Q9WZC3  (SPEH_THEMA) -  S-adenosylmethionine decarboxylase proenzyme from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 130 a.a.

Struc: 56 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains B, A, D, C: E.C.4.1.1.50 - adenosylmethionine decarboxylase.
• Pathway: Spermine Biosynthesis
• Reaction: S-adenosyl-L-methionine + H⁺ = S-adenosyl 3-(methylsulfanyl)propylamine + CO2

S-adenosyl-L-methionine + H(+) (Bound ligand (Het Group name = SMM) matches with 96.43% similarity) = S-adenosyl 3-(methylsulfanyl)propylamine + CO2

• Cofactor: Pyruvate

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

reference

DOI no: 10.1107/S090744490904877X

Acta Crystallogr D Biol Crystallogr 66:181-189 (2010)

PubMed id: 20124698

Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity.

S.Bale, K.Baba, D.E.McCloskey, A.E.Pegg, S.E.Ealick.

ABSTRACT

The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5'-deoxy-5'-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues from both chains of the homodimer. The complexes provide insights into the substrate specificity and ligand binding of AdoMetDC in prokaryotes. The conservation of the ligand-binding mode and the active-site residues between human and T. maritima AdoMetDC provides insight into the evolution of AdoMetDC.

Selected figure(s)

Figure 4.
Figure 4 Schematic view of the interactions of MeAdoMet in the active site of TmAdoMetDC.

Figure 7.
Figure 7 Stereoview of a comparison of the active sites of TmAdoMetDC (C atoms colored green) and hAdoMetDC (C atoms colored cyan) with MeAdoMet bound. Hydrogen bonds are omitted for clarity.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2010, 66, 181-189) copyright 2010.

Figures were selected by an automated process.