This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1pda
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1pda |SIZE=350|CAPTION= <scene name='initialview01'>1pda</scene>, resolution 1.76Å | |PDB= 1pda |SIZE=350|CAPTION= <scene name='initialview01'>1pda</scene>, resolution 1.76Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=DPM:3-{2-[4-(2-CARBOXY-ETHYL)-3-CARBOXYMETHYL-5H-PYRROL-2-YLMETHYL]-4-CARBOXYMETHYL-5-METHYL-2H-PYRROL-3-YL}-PROPIONIC+ACID'>DPM</scene> | + | |LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=DPM:3-{2-[4-(2-CARBOXY-ETHYL)-3-CARBOXYMETHYL-5H-PYRROL-2-YLMETHYL]-4-CARBOXYMETHYL-5-METHYL-2H-PYRROL-3-YL}-PROPIONIC+ACID'>DPM</scene> |
| - | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxymethylbilane_synthase Hydroxymethylbilane synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.61 2.5.1.61] </span> | |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pda OCA], [http://www.ebi.ac.uk/pdbsum/1pda PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pda RCSB]</span> | ||
}} | }} | ||
| Line 32: | Line 35: | ||
[[Category: Wood, S P.]] | [[Category: Wood, S P.]] | ||
[[Category: Woodcock, S C.]] | [[Category: Woodcock, S C.]] | ||
| - | [[Category: ACY]] | ||
| - | [[Category: DPM]] | ||
[[Category: lyase(porphyrin)]] | [[Category: lyase(porphyrin)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:58:07 2008'' |
Revision as of 19:58, 30 March 2008
| |||||||
| , resolution 1.76Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Hydroxymethylbilane synthase, with EC number 2.5.1.61 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE
Overview
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.
About this Structure
1PDA is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site., Louie GV, Brownlie PD, Lambert R, Cooper JB, Blundell TL, Wood SP, Warren MJ, Woodcock SC, Jordan PM, Nature. 1992 Sep 3;359(6390):33-9. PMID:1522882
Page seeded by OCA on Sun Mar 30 22:58:07 2008
