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PDBsum entry 1f2d

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1f2d
Jmol
Contents
Protein chains
341 a.a. *
Ligands
SO4 ×4
PLP ×4
Waters ×939
* Residue conservation analysis
PDB id:
1f2d
Name: Lyase
Title: 1-aminocyclopropane-1-carboxylate deaminase
Structure: 1-aminocyclopropane-1-carboxylate deaminase. Chain: a, b, c, d. Engineered: yes
Source: Williopsis saturnus. Organism_taxid: 4906. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.00Å     R-factor:   0.221     R-free:   0.268
Authors: M.Yao,T.Ose,H.Sugimoto,A.Horiuchi,A.Nakagawa,D.Yokoi,T.Murak M.Honma,S.Wakatsuki,I.Tanaka
Key ref:
M.Yao et al. (2000). Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus. J Biol Chem, 275, 34557-34565. PubMed id: 10938279 DOI: 10.1074/jbc.M004681200
Date:
24-May-00     Release date:   20-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7M523  (1A1D_CYBSA) -  1-aminocyclopropane-1-carboxylate deaminase
Seq:
Struc:
341 a.a.
341 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.5.99.7  - 1-aminocyclopropane-1-carboxylate deaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + NH3
1-aminocyclopropane-1-carboxylate
+ H(2)O
= 2-oxobutanoate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     amine catabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M004681200 J Biol Chem 275:34557-34565 (2000)
PubMed id: 10938279  
 
 
Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus.
M.Yao, T.Ose, H.Sugimoto, A.Horiuchi, A.Nakagawa, S.Wakatsuki, D.Yokoi, T.Murakami, M.Honma, I.Tanaka.
 
  ABSTRACT  
 
The pyridoxal 5'-phosphate (PLP)-dependent enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD) catalyzes a reaction that involves a ring opening of cyclopropanoid amino acid, yielding alpha-ketobutyrate and ammonia. Unlike other PLP-dependent enzymes, this enzyme has no alpha-hydrogen atom in the substrate. Thus, a unique mechanism for the bond cleavage is expected. The crystal structure of ACCD from Hansenula saturnus has been determined at 2.0 A resolution by the multiple wavelength anomalous diffraction method using mercury atoms as anomalous scatterers. The model was built on the electron density map, which was obtained by the density averaging of multiple crystal forms. The final model was refined to an R-factor of 22.5% and an R(free)-factor of 26.8%. The ACCD folds into two domains, each of which has an open twisted alpha/beta structure similar to the beta-subunit of tryptophan synthase. However, in ACCD, unlike in other members of the beta family of PLP-dependent enzymes, PLP is buried deep in the molecule. The structure provides the first view of the catalytic center of the cyclopropane ring opening.
 
  Selected figure(s)  
 
Figure 8.
Fig. 8. Hydrogen bonding networks around the active site.
Figure 9.
Fig. 9. A detailed view of the PLP-binding site and proposed substrate complex. ACC is modeled on the electron density for the bound sulfoxide ion. Thin bonds are hypothetical drawings of PLP and the bound substrate (see "Reaction Mechanism").
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 34557-34565) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18548183 J.Duan, K.M.Müller, T.C.Charles, S.Vesely, and B.R.Glick (2009).
1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Genes in Rhizobia from Southern Saskatchewan.
  Microb Ecol, 57, 423-436.  
18825405 B.Todorovic, and B.R.Glick (2008).
The interconversion of ACC deaminase and D: -cysteine desulfhydrase by directed mutagenesis.
  Planta, 229, 193-205.  
18400007 C.Prigent-Combaret, D.Blaha, J.F.Pothier, L.Vial, M.A.Poirier, F.Wisniewski-Dyé, and Y.Moënne-Loccoz (2008).
Physical organization and phylogenetic analysis of acdR as leucine-responsive regulator of the 1-aminocyclopropane-1-carboxylate deaminase gene acdS in phytobeneficial Azospirillum lipoferum 4B and other Proteobacteria.
  FEMS Microbiol Ecol, 65, 202-219.  
16689877 D.Blaha, C.Prigent-Combaret, M.S.Mirza, and Y.Moënne-Loccoz (2006).
Phylogeny of the 1-aminocyclopropane-1-carboxylic acid deaminase-encoding gene acdS in phytobeneficial and pathogenic Proteobacteria and relation with strain biogeography.
  FEMS Microbiol Ecol, 56, 455-470.  
15720402 A.Riemenschneider, R.Wegele, A.Schmidt, and J.Papenbrock (2005).
Isolation and characterization of a D-cysteine desulfhydrase protein from Arabidopsis thaliana.
  FEBS J, 272, 1291-1304.  
16099604 B.R.Glick (2005).
Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase.
  FEMS Microbiol Lett, 251, 1-7.  
15890029 K.H.Jhee, and W.D.Kruger (2005).
The role of cystathionine beta-synthase in homocysteine metabolism.
  Antioxid Redox Signal, 7, 813-822.  
11344332 K.Thomazeau, G.Curien, R.Dumas, and V.Biou (2001).
Crystal structure of threonine synthase from Arabidopsis thaliana.
  Protein Sci, 10, 638-648.
PDB code: 1e5x
11483494 M.Meier, M.Janosik, V.Kery, J.P.Kraus, and P.Burkhard (2001).
Structure of human cystathionine beta-synthase: a unique pyridoxal 5'-phosphate-dependent heme protein.
  EMBO J, 20, 3910-3916.
PDB code: 1jbq
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.