3PCN

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3,4-DIHYDROXYPHENYLACETATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate.

Elgren, T.E.Orville, A.M.Kelly, K.A.Lipscomb, J.D.Ohlendorf, D.H.Que Jr., L.

(1997) Biochemistry 36: 11504-11513

  • DOI: 10.1021/bi970691k
  • Primary Citation of Related Structures:  
    3PCN

  • PubMed Abstract: 
  • The crystal structure of the anaerobic complex of Pseudomonas putida protocatechuate 3,4-dioxygenase (3,4-PCD) bound with the alternative substrate, 3,4-dihydroxyphenylacetate (HPCA), is reported at 2.4 A resolution and refined to an R factor of 0.17. Formation of the active site Fe(III) ...

    The crystal structure of the anaerobic complex of Pseudomonas putida protocatechuate 3,4-dioxygenase (3,4-PCD) bound with the alternative substrate, 3,4-dihydroxyphenylacetate (HPCA), is reported at 2.4 A resolution and refined to an R factor of 0.17. Formation of the active site Fe(III).HPCA chelated complex causes the endogenous axial tyrosinate, Tyr447 (147beta), to dissociate from the iron and rotate into an alternative orientation analogous to that previously observed in the anaerobic 3,4-PCD.3,4-dihydroxybenzoate complex (3, 4-PCD.PCA) [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066]. Two orientations of the aromatic ring of HPCA related by an approximate 180 degrees rotation within the active site are consistent with the electron density. Resonance Raman (rR) spectroscopic data from Brevibacteriumfuscum 3,4-PCD.HPCA complex in solution reveals low frequency rR vibrational bands between 500 and 650 cm-1 as well as a band at approximately 1320 cm-1 which are diagnostic of a HPCA. Fe(III) chelate complex. 18O labeling of HPCA at either the C4 or C3 hydroxyl group unambiguously establishes the vibrational coupling modes associated with the five-membered chelate ring system. Analysis of these data suggests that the Fe(III)-HPCAO4 bond is shorter than the Fe(III)-HPCAO3 bond. This consequently favors the model for the crystal structure in which the C3 phenolic function occupies the Fe3+ ligand site opposite the endogenous ligand Tyr408(Oeta) (108beta). This is essentially the same binding orientation as proposed for PCA in the crystal structure of the anaerobic 3,4-PCD.PCA complex based solely on direct modeling of the 2Fo - Fc electron density and suggests that this is the conformation required for catalysis.


    Related Citations: 
    • Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-Dioxygenase: Endogenous Fe3+ Ligand Displacement in Response to Substrate Binding
      Orville, A.M., Lipscomb, J.D., Ohlendorf, D.H.
      (1997) Biochemistry 36: 10052
    • Structures of Competitive Inhibitor Complexes of Protocatechuate 3,4-Dioxygenase: Multiple Exogenous Ligand Binding Orientations within the Active Site
      Orville, A.M., Elango, N., Lipscomb, J.D., Ohlendorf, D.H.
      (1997) Biochemistry 36: 10039
    • Structure of Protocatechuate 3,4-Dioxygenase from Pseudomonas Aeruginosa at 2.15 A Resolution
      Ohlendorf, D.H., Orville, A.M., Lipscomb, J.D.
      (1994) J Mol Biol 244: 586
    • Structure and Assembly of Protocatechuate 3,4-Dioxygenase
      Ohlendorf, D.H., Lipscomb, J.D., Weber, P.C.
      (1988) Nature 336: 403

    Organizational Affiliation

    Department of Chemistry, Hamilton College, Clinton, New York 13323, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASE200Pseudomonas putidaMutation(s): 0 
Gene Names: pcaG
EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida)
Explore P00436 
Go to UniProtKB:  P00436
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00436
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASE238Pseudomonas putidaMutation(s): 0 
Gene Names: pcaH
EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida)
Explore P00437 
Go to UniProtKB:  P00437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00437
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHY
Query on DHY

Download Ideal Coordinates CCD File 
AA [auth Q],
DA [auth R],
O [auth M],
R [auth N],
U [auth O],
AA [auth Q],
DA [auth R],
O [auth M],
R [auth N],
U [auth O],
X [auth P]
2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
C8 H8 O4
CFFZDZCDUFSOFZ-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
CA [auth R],
N [auth M],
Q [auth N],
T [auth O],
W [auth P],
CA [auth R],
N [auth M],
Q [auth N],
T [auth O],
W [auth P],
Z [auth Q]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
BA [auth R],
M,
P [auth N],
S [auth O],
V [auth P],
BA [auth R],
M,
P [auth N],
S [auth O],
V [auth P],
Y [auth Q]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DHY PDBBind:  3PCN Kd: 2.20e+5 (nM) from 1 assay(s)
Binding MOAD:  3PCN Kd: 2.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.166 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.6α = 90
b = 127.5β = 97.7
c = 134.3γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-02-25
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance