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PDBsum entry 1yjl

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protein links
Oxidoreductase PDB id
1yjl
Jmol
Contents
Protein chain
285 a.a. *
Waters ×46
* Residue conservation analysis
PDB id:
1yjl
Name: Oxidoreductase
Title: Reduced peptidylglycine alpha-hydroxylating monooxygenase in a new crystal form
Structure: Peptidyl-glycine alpha-amidating monooxygenase. Chain: a. Fragment: peptidylglycine alpha-hydroxylating monooxygenase (residues 50-355). Synonym: pam. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: pam. Expressed in: cricetulus griseus. Expression_system_taxid: 10029.
Resolution:
2.40Å     R-factor:   0.209     R-free:   0.274
Authors: X.Siebert,B.A.Eipper,R.E.Mains,S.T.Prigge,N.J.Blackburn, L.M.Amzel
Key ref: X.Siebert et al. (2005). The catalytic copper of peptidylglycine alpha-hydroxylating monooxygenase also plays a critical structural role. Biophys J, 89, 3312-3319. PubMed id: 16100265
Date:
14-Jan-05     Release date:   15-Nov-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14925  (AMD_RAT) -  Peptidyl-glycine alpha-amidating monooxygenase
Seq:
Struc:
 
Seq:
Struc:
976 a.a.
285 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.1.14.17.3  - Peptidylglycine monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylglycine + ascorbate + O2 = peptidyl(2-hydroxyglycine) + dehydroascorbate + H2O
Peptidylglycine
+ ascorbate
+ O(2)
= peptidyl(2-hydroxyglycine)
+ dehydroascorbate
+ H(2)O
      Cofactor: Cu cation
   Enzyme class 2: E.C.4.3.2.5  - Peptidylamidoglycolate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylamidoglycolate = peptidyl amide + glyoxylate
Peptidylamidoglycolate
= peptidyl amide
+ glyoxylate
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     membrane   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
Biophys J 89:3312-3319 (2005)
PubMed id: 16100265  
 
 
The catalytic copper of peptidylglycine alpha-hydroxylating monooxygenase also plays a critical structural role.
X.Siebert, B.A.Eipper, R.E.Mains, S.T.Prigge, N.J.Blackburn, L.M.Amzel.
 
  ABSTRACT  
 
Many bioactive peptides require amidation of their carboxy terminus to exhibit full biological activity. Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3), the enzyme that catalyzes the first of the two steps of this reaction, is composed of two domains, each of which binds one copper atom (CuH and CuM). The CuM site includes Met(314) and two His residues as ligands. Mutation of Met(314) to Ile inactivates PHM, but has only a minimal effect on the EXAFS spectrum of the oxidized enzyme, implying that it contributes only marginally to stabilization of the CuM site. To characterize the role of Met(314) as a CuM ligand, we determined the structure of the Met(314)Ile-PHM mutant. Since the mutant protein failed to crystallize in the conditions of the original wild-type protein, this structure determination required finding a new crystal form. The Met(314)Ile-PHM mutant structure confirms that the mutation does not abolish CuM binding to the enzyme, but causes other structural perturbations that affect the overall stability of the enzyme and the integrity of the CuH site. To eliminate possible effects of crystal contacts, we redetermined the structure of wt-PHM in the Met(314)Ile-PHM crystal form and showed that it does not differ from the structure of wild-type (wt)-PHM in the original crystals. Met(314)Ile-PHM was also shown to be less stable than wt-PHM by differential scanning calorimetry. Both structural and calorimetric studies point to a structural role for the CuM site, in addition to its established catalytic role.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544364 C.R.Hess, J.P.Klinman, and N.J.Blackburn (2010).
The copper centers of tyramine β-monooxygenase and its catalytic-site methionine variants: an X-ray absorption study.
  J Biol Inorg Chem, 15, 1195-1207.  
20648645 D.Bousquet-Moore, R.E.Mains, and B.A.Eipper (2010).
Peptidylgycine alpha-amidating monooxygenase and copper: a gene-nutrient interaction critical to nervous system function.
  J Neurosci Res, 88, 2535-2545.  
20715282 E.Langella, S.Pierre, W.Ghattas, M.Giorgi, M.Réglier, M.Saviano, L.Esposito, and R.Hardré (2010).
Probing the peptidylglycine alpha-hydroxylating monooxygenase active site with novel 4-phenyl-3-butenoic acid based inhibitors.
  ChemMedChem, 5, 1568-1576.  
20423905 L.M.Iyer, S.Abhiman, R.F.de Souza, and L.Aravind (2010).
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase.
  Nucleic Acids Res, 38, 5261-5279.  
17005911 J.A.Sobota, F.Ferraro, N.Bäck, B.A.Eipper, and R.E.Mains (2006).
Not all secretory granules are created equal: Partitioning of soluble content proteins.
  Mol Biol Cell, 17, 5038-5052.  
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.