1PDA

STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE

Summary for 1PDA

• Entry DOI: 10.2210/pdb1pda/pdb
• Descriptor: PORPHOBILINOGEN DEAMINASE, 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: porphyrin, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 34372.27

Authors

Louie, G.V.,Brownlie, P.D.,Lambert, R.,Cooper, J.B.,Blundell, T.L.,Wood, S.P.,Warren, M.J.,Woodcock, S.C.,Jordan, P.M. (deposition date: 1992-11-17, release date: 1993-10-31, Last modification date: 2019-08-14)

Primary citation

Louie, G.V.,Brownlie, P.D.,Lambert, R.,Cooper, J.B.,Blundell, T.L.,Wood, S.P.,Warren, M.J.,Woodcock, S.C.,Jordan, P.M.
Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.
Nature, 359:33-39, 1992

PubMed Abstract: The three-domain structure of porphobilinogen deaminase, a key enzyme in the biosynthetic pathway of tetrapyrroles, has been defined by X-ray analysis at 1.9 A resolution. Two of the domains structurally resemble the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins. The X-ray structure and results from site-directed mutagenesis provide evidence for a single catalytic site. Interdomain flexibility may aid elongation of the polypyrrole product in the active-site cleft of the enzyme.

PubMed: 1522882
DOI: 10.1038/359033a0

Experimental method

X-RAY DIFFRACTION (1.76 Å)