Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates.

Frazee, R.W.Orville, A.M.Dolbeare, K.B.Yu, H.Ohlendorf, D.H.Lipscomb, J.D.

(1998) Biochemistry 37: 2131-2144

  • DOI: 10.1021/bi972047b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The essential active site Fe3+ of protocatechuate 3,4-dioxygenase [3, 4-PCD, subunit structure (alphabetaFe3+)12] is bound by axial ligands, Tyr447 (147beta) and His462 (162beta), and equatorial ligands, Tyr408 (108beta), His460 (160beta), and a solvent OH- (Wat827) ...

    The essential active site Fe3+ of protocatechuate 3,4-dioxygenase [3, 4-PCD, subunit structure (alphabetaFe3+)12] is bound by axial ligands, Tyr447 (147beta) and His462 (162beta), and equatorial ligands, Tyr408 (108beta), His460 (160beta), and a solvent OH- (Wat827). Recent X-ray crystallographic studies have shown that Tyr447 is dissociated from the Fe3+ in the anaerobic 3,4-PCD complex with protocatechuate (PCA) [Orville, A. M., Lipscomb, J. D., and Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066]. The importance of Tyr447 to catalysis is investigated here by site-directed mutation of this residue to His (Y447H), the first such mutation reported for an aromatic ring cleavage dioxygenase containing Fe3+. The crystal structure of Y447H (2.1 A resolution, R-factor of 0.181) is essentially unchanged from that of the native enzyme outside of the active site region. The side chain position of His447 is stabilized by a His447(N)delta1-Pro448(O) hydrogen bond, placing the Nepsilon2 atom of His447 out of bonding distance of the iron ( approximately 4.3 A). Wat827 appears to be replaced by a CO32-, thereby retaining the overall charge neutrality and coordination number of the Fe3+ center. Quantitative metal and amino acid analysis shows that Y447H binds Fe3+ in approximately 10 of the 12 active sites of 3,4-PCD, but its kcat is nearly 600-fold lower than that of the native enzyme. Single-turnover kinetic analysis of the Y447H-catalyzed reaction reveals that slow substrate binding accounts for the decreased kcat. Three new kinetically competent intermediates in this process are revealed. Similarly, the product dissociation from Y447H is slow and occurs in two resolved steps, including a previously unreported intermediate. The final E.PCA complex (ES4) and the putative E.product complex (ESO2*) are found to have optical spectra that are indistinguishable from those of the analogous intermediates of the wild-type enzyme cycle, while all of the other observed intermediates have novel spectra. Once the E.S complex is formed, reaction with O2 is fast. These results suggest that dissociation of Tyr447 occurs during turnover of 3,4-PCD and is important in the substrate binding and product release processes. Once Tyr447 is removed from the Fe3+ in the final E.PCA complex by either dissociation or mutagenesis, the O2 attack and insertion steps proceed efficiently, suggesting that Tyr447 does not have a large role in this phase of the reaction. This study demonstrates a novel role for Tyr in a biological system and allows evaluation and refinement of the proposed Fe3+ dioxygenase mechanism.

    Related Citations: 
    • 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 Junior, L.
      (1997) Biochemistry 36: 11504
    • 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 Biochemistry, Medical School, and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASEA, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]200Pseudomonas putidaMutation(s): 0 
Gene Names: PCAHpcaG
Find proteins for P00436 (Pseudomonas putida)
Explore P00436 
Go to UniProtKB:  P00436
Protein Feature View
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASEB [auth M], D [auth N], F [auth O], H [auth P], J [auth Q], L [auth R]238Pseudomonas putidaMutation(s): 1 
Gene Names: pcaH
Find proteins for P00437 (Pseudomonas putida)
Explore P00437 
Go to UniProtKB:  P00437
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on BME

Download Ideal Coordinates CCD File 
AA [auth Q], DA [auth R], O [auth M], R [auth N], U [auth O], X [auth P]BETA-MERCAPTOETHANOL
C2 H6 O S
 Ligand Interaction
Query on CO3

Download Ideal Coordinates CCD File 
BA [auth R], M, P [auth N], S [auth O], V [auth P], Y [auth Q]CARBONATE ION
C O3
 Ligand Interaction
Query on FE

Download Ideal Coordinates CCD File 
CA [auth R], N [auth M], Q [auth N], T [auth O], W [auth P], Z [auth Q]FE (III) ION
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Work: 0.180 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.4α = 90
b = 127.2β = 97.7
c = 134.6γ = 90
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    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