1PDA | pdb_00001pda

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

• PDB DOI: https://doi.org/10.2210/pdb1PDA/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1992-11-17 Released: 1993-10-31 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Work: 
  0.188 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.

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.

(1992) Nature 359: 33-39

• PubMed: 1522882 
• DOI: https://doi.org/10.1038/359033a0
• Primary Citation Related Structures: 
  1PDA


• 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.

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Organizational Affiliation: 
• Department of Crystallography, Birkbeck College, University of London, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2,527 
• Modeled Residue Count: 296 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PORPHOBILINOGEN DEAMINASE	A	313	Escherichia coli	Mutation(s): 0  EC: 2.5.1.61
UniProt
Find proteins for P06983 (Escherichia coli (strain K12)) Explore P06983  Go to UniProtKB:  P06983

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPM	B [auth A]	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid C20 H24 N2 O8 LCAXMKQKEYTFDM-UHFFFAOYSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Work:  0.188 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88	α = 90
b = 75.9	β = 90
c = 50.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-09-18
  Changes: Non-polymer description
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.7: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary