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PDBsum entry 2d3t

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protein ligands Protein-protein interface(s) links
Lyase, oxidoreductase/transferase PDB id
2d3t
Jmol
Contents
Protein chains
708 a.a. *
390 a.a. *
Ligands
ACO ×2
NAD ×2
* Residue conservation analysis
PDB id:
2d3t
Name: Lyase, oxidoreductase/transferase
Title: Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form v
Structure: Fatty oxidation complex alpha subunit. Chain: a, b. Ec: 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3. Engineered: yes. 3-ketoacyl-coa thiolase. Chain: c, d. Synonym: fatty oxidation complex beta subunit, beta- ketothiolase, acetyl-coa acyltransferase. Engineered: yes
Source: Pseudomonas fragi. Organism_taxid: 296. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
3.40Å     R-factor:   0.242     R-free:   0.295
Authors: D.Tsuchiya,N.Shimizu,M.Ishikawa,Y.Suzuki,K.Morikawa
Key ref:
D.Tsuchiya et al. (2006). Ligand-Induced Domain Rearrangement of Fatty Acid beta-Oxidation Multienzyme Complex. Structure, 14, 237-246. PubMed id: 16472743 DOI: 10.1016/j.str.2005.10.011
Date:
01-Oct-05     Release date:   21-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28793  (FADB_PSEFR) -  Fatty acid oxidation complex subunit alpha
Seq:
Struc:
 
Seq:
Struc:
715 a.a.
708 a.a.
Protein chains
Pfam   ArchSchema ?
P28790  (FADA_PSEFR) -  3-ketoacyl-CoA thiolase
Seq:
Struc:
391 a.a.
390 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.1.1.1.35  - 3-hydroxyacyl-CoA dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH
(S)-3-hydroxyacyl-CoA
Bound ligand (Het Group name = ACO)
matches with 94.00% similarity
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= 3-oxoacyl-CoA
+ NADH
   Enzyme class 2: Chains A, B: E.C.4.2.1.17  - Enoyl-CoA hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H2O
(3S)-3-hydroxyacyl-CoA
Bound ligand (Het Group name = ACO)
matches with 94.00% similarity
= trans-2(or 3)-enoyl-CoA
+ H(2)O
   Enzyme class 3: Chains A, B: E.C.5.1.2.3  - 3-hydroxybutyryl-CoA epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-3-hydroxybutanoyl-CoA = (R)-3-hydroxybutanoyl-CoA
(S)-3-hydroxybutanoyl-CoA
Bound ligand (Het Group name = ACO)
matches with 94.00% similarity
= (R)-3-hydroxybutanoyl-CoA
   Enzyme class 4: Chains A, B: E.C.5.3.3.8  - Dodecenoyl-CoA isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3Z)-dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA
(3Z)-dodec-3-enoyl-CoA
Bound ligand (Het Group name = ACO)
matches with 83.00% similarity
= (2E)-dodec-2-enoyl-CoA
   Enzyme class 5: Chains C, D: E.C.2.3.1.16  - Acetyl-CoA C-acyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA
Acyl-CoA
+
acetyl-CoA
Bound ligand (Het Group name = ACO)
corresponds exactly
= CoA
+ 3-oxoacyl-CoA
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     fatty acid beta-oxidation multienzyme complex   2 terms 
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     15 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2005.10.011 Structure 14:237-246 (2006)
PubMed id: 16472743  
 
 
Ligand-Induced Domain Rearrangement of Fatty Acid beta-Oxidation Multienzyme Complex.
D.Tsuchiya, N.Shimizu, M.Ishikawa, Y.Suzuki, K.Morikawa.
 
  ABSTRACT  
 
The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Substrate Recognition in the a Subunit
(A) Local structures around the adenine base binding site in the a subunit, observed in forms I (red) and V (orange, green). The bound ligand is acetyl-CoA, which is an analog of 3-hydroxyacyl-CoA.
(B and C) The corresponding structures of the (B) proximal and (C) distal subunits in form II.
(D) Superimposition of the two a subunits in the apparently symmetric form I, in which the acetyl-CoA (the red space-filling model) was observed. The ligand bound subunit (red) is more open than the unliganded one (blue). As a consequence, only the aC domain exhibits a significant difference. The circle with the broken line indicates the adenine base moiety in (A).
 
  The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 237-246) copyright 2006.  
  Figure was selected by an automated process.