4HTG

Porphobilinogen Deaminase from Arabidopsis Thaliana

PDB DOI: 10.2210/pdb4HTG/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-01 Released: 2013-02-27
Deposition Author(s): Roberts, A., Gill, R., Hussey, R.J., Erskine, P.T., Cooper, J.B., Wood, S.P., Chrystal, E.J.T., Shoolingin-Jordan, P.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.217
R-Value Work: 0.145
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme.

Roberts, A., Gill, R., Hussey, R.J., Mikolajek, H., Erskine, P.T., Cooper, J.B., Wood, S.P., Chrystal, E.J., Shoolingin-Jordan, P.M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 471-485

PubMed: 23519422 Search on PubMed
DOI: 10.1107/S0907444912052134
Primary Citation of Related Structures:
4HTG

PubMed Abstract:

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem- and chlorophyll-biosynthesis pathways in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The active site possesses an unusual dipyrromethane cofactor which is extended during the reaction by the sequential addition of the four substrate molecules. The cofactor is linked covalently to the enzyme through a thioether bridge to the invariant Cys254. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. The expression of a codon-optimized gene for PBGD from Arabidopsis thaliana (thale cress) has permitted for the first time the X-ray analysis of the enzyme from a higher plant species at 1.45 Å resolution. The A. thaliana structure differs appreciably from the E. coli and human forms of the enzyme in that the active site is shielded by an extensive well defined loop region (residues 60-70) formed by highly conserved residues. This loop is completely disordered and uncharacterized in the E. coli and human PBGD structures. The new structure establishes that the dipyrromethane cofactor of the enzyme has become oxidized to the dipyrromethenone form, with both pyrrole groups approximately coplanar. Modelling of an intermediate of the elongation process into the active site suggests that the interactions observed between the two pyrrole rings of the cofactor and the active-site residues are highly specific and are most likely to represent the catalytically relevant binding mode. During the elongation cycle, it is thought that domain movements cause the bound cofactor and polypyrrole intermediates to move past the catalytic machinery in a stepwise manner, thus permitting the binding of additional substrate moieties and completion of the tetrapyrrole product. Such a model would allow the condensation reactions to be driven by the extensive interactions that are observed between the enzyme and the dipyrromethane cofactor, coupled with acid-base catalysis provided by the invariant aspartate residue Asp95.

Organizational Affiliation:

School of Biological Sciences, University of Southampton, Southampton SO16 1BJ, England.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Porphobilinogen deaminase, chloroplastic	A	320	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At5g08280, F8L15_10, HEMC, RUG1 EC: 2.5.1.61
UniProt
Find proteins for Q43316 (Arabidopsis thaliana) Explore Q43316 Go to UniProtKB: Q43316
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q43316
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
18W Query on 18W Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3-[(5Z)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methylidene}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid C₂₀ H₂₂ N₂ O₉ MBSNQHZDABRTAT-NVNXTCNLSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction