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PDBsum entry 3pcb
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protein ligands metals Protein-protein interface(s) links
Dioxygenase PDB id
3pcb

 

 

 

 

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Contents
Protein chains
(+ 0 more) 200 a.a. *
(+ 0 more) 233 a.a. *
Ligands
3HB ×12
Metals
_FE ×6
Waters ×1416
* Residue conservation analysis
PDB id:
3pcb
Name: Dioxygenase
Title: Structure of protocatechuate 3,4-dioxygenase complexed with 3- hydroxybenzoate
Structure: Protocatechuate 3,4-dioxygenase alpha chain. Chain: a, b, c, d, e, f. Synonym: 3,4-pcd. Other_details: entry contains alpha/beta 6-mer. Protocatechuate 3,4-dioxygenase beta chain. Chain: m, n, o, p, q, r. Synonym: 3,4-pcd. Other_details: entry contains alpha/beta 6-mer
Source: Pseudomonas putida. Organism_taxid: 303. Atcc: 23975. Atcc: 23975
Biol. unit: 24mer (from PDB file)
Resolution:
2.19Å     R-factor:   0.159    
Authors: N.Elango,A.M.Orville,J.D.Lipscomb,D.H.Ohlendorf
Key ref:
A.M.Orville et al. (1997). Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site. Biochemistry, 36, 10039-10051. PubMed id: 9254599 DOI: 10.1021/bi970468n
Date:
25-Apr-97     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00436  (PCXA_PSEPU) -  Protocatechuate 3,4-dioxygenase alpha chain from Pseudomonas putida
Seq:
Struc: 		201 a.a.
200 a.a.
Protein chains
Pfam   ArchSchema ?
P00437  (PCXB_PSEPU) -  Protocatechuate 3,4-dioxygenase beta chain from Pseudomonas putida
Seq:
Struc: 		239 a.a.
233 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, M, B, N, C, O, D, P, E, Q, F, R: E.C.1.13.11.3  - protocatechuate 3,4-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Benzoate Metabolism
      Reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate + 2 H+
3,4-dihydroxybenzoate
Bound ligand (Het Group name = 3HB)
matches with 90.91% similarity 		+ O2
 = 3-carboxy-cis,cis-muconate
 + 2 × H(+)
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi970468n Biochemistry 36:10039-10051 (1997)
PubMed id: 9254599  
 
 
Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site.
A.M.Orville, N.Elango, J.D.Lipscomb, D.H.Ohlendorf.
 
  ABSTRACT  
 
Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary structure of (alphabetaFe3+)12] complexed with seven competitive inhibitors [3-hydroxyphenylacetate (MHP), 4-hydroxyphenylacetate (PHP), 3-hydroxybenzoate (MHB), 4-hydroxybenzoate (PHB), 3-fluoro-4-hydroxybenzoate (FHB), 3-chloro-4-hydroxybenzoate (CHB), and 3-iodo-4-hydroxybenzoate (IHB)] are reported at 2.0-2.2 A resolution with R-factors of 0. 0.159-0.179. The inhibitors bind in a narrow active site crevasse lined with residues that provide a microenvironment that closely matches the chemical characteristics of the inhibitors. This results in as little as 20% solvent-exposed surface area for the higher-affinity inhibitors (PHB, CHB, and FHB). In uncomplexed 3,4-PCD, the active site Fe3+ is bound at the bottom of the active site crevasse by four endogenous ligands and a solvent molecule (Wat827). The orientations of the endogenous ligands are relatively unperturbed in each inhibitor complex, but the inhibitors themselves bind to or near the iron in a range of positions, all of which perturb the position of Wat827. The three lowest-affinity inhibitors (MHP, PHP, and IHB) yield distorted trigonal bipyramidal iron coordination geometry in which the inhibitor C4-phenolate group displaces the solvent ligand. MHB binds within the active site, but neither its C3-OH group nor the solvent molecule binds to the iron. The C4-phenolate group of the three highest-affinity inhibitors (PHB, CHB, and FHB) coordinates the Fe3+ adjacent to Wat827, resulting in a shift in its position to yield a six-coordinate distorted octahedral geometry. The range of inhibitor orientations may mimic the mechanistically significant stages of substrate binding to 3, 4-PCD. The structure of the final substrate complex is reported in the following paper [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066].
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20835480 R.Mayilmurugan, M.Sankaralingam, E.Suresh, and M.Palaniandavar (2010).
Novel square pyramidal iron(III) complexes of linear tetradentate bis(phenolate) ligands as structural and reactive models for intradiol-cleaving 3,4-PCD enzymes: Quinone formation vs. intradiol cleavage.
  Dalton Trans, 39, 9611-9625.  
19368882 D.L.Mobley, and K.A.Dill (2009).
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
  Structure, 17, 489-498.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
18003930 M.Y.Pau, J.D.Lipscomb, and E.I.Solomon (2007).
Substrate activation for O2 reactions by oxidized metal centers in biology.
  Proc Natl Acad Sci U S A, 104, 18355-18362.  
17256852 M.Y.Pau, M.I.Davis, A.M.Orville, J.D.Lipscomb, and E.I.Solomon (2007).
Spectroscopic and electronic structure study of the enzyme-substrate complex of intradiol dioxygenases: substrate activation by a high-spin ferric non-heme iron site.
  J Am Chem Soc, 129, 1944-1958.  
15772073 M.Ferraroni, J.Seifert, V.M.Travkin, M.Thiel, S.Kaschabek, A.Scozzafava, L.Golovleva, M.Schlömann, and F.Briganti (2005).
Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation.
  J Biol Chem, 280, 21144-21154.
PDB code: 1tmx
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
15487948 C.K.Brown, M.W.Vetting, C.A.Earhart, and D.H.Ohlendorf (2004).
Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1.
  Annu Rev Microbiol, 58, 555-585.
PDB codes: 2bum 2buq 2bur 2but 2buv
15060064 M.Ferraroni, I.P.Solyanikova, M.P.Kolomytseva, A.Scozzafava, L.Golovleva, and F.Briganti (2004).
Crystal structure of 4-chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing gram-positive Rhodococcus opacus 1CP.
  J Biol Chem, 279, 27646-27655.
PDB code: 1s9a
11208799 T.Potrawfke, J.Armengaud, and R.M.Wittich (2001).
Chlorocatechols substituted at positions 4 and 5 are substrates of the broad-spectrum chlorocatechol 1,2-dioxygenase of Pseudomonas chlororaphis RW71.
  J Bacteriol, 183, 997.  
10891075 M.W.Vetting, D.A.D'Argenio, L.N.Ornston, and D.H.Ohlendorf (2000).
Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase.
  Biochemistry, 39, 7943-7955.
PDB codes: 1eo2 1eo9 1eoa 1eob 1eoc
10801478 M.W.Vetting, and D.H.Ohlendorf (2000).
The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
  Structure, 8, 429-440.
PDB codes: 1dlm 1dlq 1dlt 1dmh
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
  Curr Opin Struct Biol, 9, 722-731.  
  10515940 D.A.D'Argenio, M.W.Vetting, D.H.Ohlendorf, and L.N.Ornston (1999).
Substitution, insertion, deletion, suppression, and altered substrate specificity in functional protocatechuate 3,4-dioxygenases.
  J Bacteriol, 181, 6478-6487.  
10545093 F.X.Gomis-Rüth, V.Companys, Y.Qian, L.D.Fricker, J.Vendrell, F.X.Avilés, and M.Coll (1999).
Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase subfamily.
  EMBO J, 18, 5817-5826.
PDB code: 1qmu
10467151 K.Sugimoto, T.Senda, H.Aoshima, E.Masai, M.Fukuda, and Y.Mitsui (1999).
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
  Structure, 7, 953-965.
PDB codes: 1b4u 1bou
10194363 S.K.Lee, and J.D.Lipscomb (1999).
Oxygen activation catalyzed by methane monooxygenase hydroxylase component: proton delivery during the O-O bond cleavage steps.
  Biochemistry, 38, 4423-4432.  
9667942 A.J.Thomson, and H.B.Gray (1998).
Bio-inorganic chemistry
  Curr Opin Chem Biol, 2, 155-158.  
9485360 R.W.Frazee, A.M.Orville, K.B.Dolbeare, H.Yu, D.H.Ohlendorf, and J.D.Lipscomb (1998).
The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates.
  Biochemistry, 37, 2131-2144.
PDB code: 3pcd
9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
  Curr Opin Chem Biol, 2, 159-172.  
9254600 A.M.Orville, J.D.Lipscomb, and D.H.Ohlendorf (1997).
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
  Biochemistry, 36, 10052-10066.
PDB codes: 3pca 3pcj 3pck 3pcl 3pcm
9369476 A.M.Orville, and J.D.Lipscomb (1997).
Cyanide and nitric oxide binding to reduced protocatechuate 3,4-dioxygenase: insight into the basis for order-dependent ligand binding by intradiol catecholic dioxygenases.
  Biochemistry, 36, 14044-14055.  
9298971 T.E.Elgren, A.M.Orville, K.A.Kelly, J.D.Lipscomb, D.H.Ohlendorf, and L.Que (1997).
Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate.
  Biochemistry, 36, 11504-11513.
PDB code: 3pcn
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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