1PDA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1038/359033a0

  • 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 bind ...

    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.


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, University of London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PORPHOBILINOGEN DEAMINASE
A
313Escherichia coli (strain K12)Gene Names: hemC (popE)
EC: 2.5.1.61
Find proteins for P06983 (Escherichia coli (strain K12))
Go to UniProtKB:  P06983
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
DPM
Query on DPM

Download SDF File 
Download CCD File 
A
3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
DIPYRROMETHANE COFACTOR
C20 H24 N2 O8
LCAXMKQKEYTFDM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.000α = 90.00
b = 75.900β = 90.00
c = 50.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
PROLSQrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-09-18
    Type: Non-polymer description
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other