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PDBsum entry 1ryc
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protein ligands links
Oxidoreductase PDB id
1ryc

 

 

 

 

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Contents
Protein chain
291 a.a. *
Ligands
HEM
BZI
Waters ×117
* Residue conservation analysis
PDB id:
1ryc
Name: Oxidoreductase
Title: CytochromE C peroxidase w191g from saccharomyces cerevisiae
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.80Å     R-factor:   0.163    
Authors: M.M.Fitzgerald,R.Musah,D.E.Mcree,D.B.Goodin
Key ref: M.M.Fitzgerald et al. (1996). A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity. Nat Struct Biol, 3, 626-631. PubMed id: 8673607
Date:
10-May-96     Release date:   08-Nov-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		361 a.a.
291 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.5  - cytochrome-c peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 Fe(II)-[cytochrome c] + H2O2 + 2 H+ = 2 Fe(III)-[cytochrome c] + 2 H2O
2 × Fe(II)-[cytochrome c]
 + H2O2
 + 2 × H(+)
 = 2 × Fe(III)-[cytochrome c]
 + 2 × H2O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Nat Struct Biol 3:626-631 (1996)
PubMed id: 8673607  
 
 
A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.
M.M.Fitzgerald, R.A.Musah, D.E.McRee, D.B.Goodin.
 
  ABSTRACT  
 
Conformational changes that gate the access of substrates or ligands to an active site are important features of enzyme function. In this report, we describe an unusual example of a structural rearrangement near a buried artificial cavity in cytochrome c peroxidase that occurs on binding protonated benzimidazole. A hinged main-chain rotation at two residues (Pro 190 and Asn 195) results in a surface loop rearrangement that opens a large solvent-accessible channel for the entry of ligands to an otherwise inaccessible binding site. The trapping of this alternate conformational state provides a unique view of the extent to which protein dynamics can allow small molecule penetration into buried protein cavities.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18418822 R.Baron, and J.A.McCammon (2008).
(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.
  Chemphyschem, 9, 983-988.  
18196463 R.E.Amaro, R.Baron, and J.A.McCammon (2008).
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
  J Comput Aided Mol Des, 22, 693-705.  
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.  
16372349 K.Bastard, C.Prévost, and M.Zacharias (2006).
Accounting for loop flexibility during protein-protein docking.
  Proteins, 62, 956-969.  
16490206 R.Brenk, S.W.Vetter, S.E.Boyce, D.B.Goodin, and B.K.Shoichet (2006).
Probing molecular docking in a charged model binding site.
  J Mol Biol, 357, 1449-1470.
PDB codes: 2anz 2aqd 2as1 2as2 2as3 2as4 2as6 2eun 2euo 2eup 2euq 2eur 2eus 2eut 2euu
16043718 R.Murali, X.Cheng, A.Berezov, X.Du, A.Schön, E.Freire, X.Xu, Y.H.Chen, and M.I.Greene (2005).
Disabling TNF receptor signaling by induced conformational perturbation of tryptophan-107.
  Proc Natl Acad Sci U S A, 102, 10970-10975.  
12538891 A.M.Hays, H.B.Gray, and D.B.Goodin (2003).
Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.
  Protein Sci, 12, 278-287.  
11967381 R.J.Rosenfeld, A.M.Hays, R.A.Musah, and D.B.Goodin (2002).
Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.
  Protein Sci, 11, 1251-1259.
PDB codes: 1kxm 1kxn
10651820 M.Kintrup, P.Schubert, M.Kunz, M.Chabbert, P.Alberti, E.Bombarda, S.Schneider, and W.Hillen (2000).
Trp scanning analysis of Tet repressor reveals conformational changes associated with operator and anhydrotetracycline binding.
  Eur J Biochem, 267, 821-829.  
10911727 M.Kunz, M.Kintrup, W.Hillen, and S.Schneider (2000).
Conformational changes induced in the Tet repressor protein TetR(B) upon operator or anhydrotetracycline binding as revealed by time-resolved fluorescence spectroscopy on single tryptophan mutants.
  Photochem Photobiol, 72, 35-48.  
  10048328 G.H.Krooshof, R.Floris, A.W.Tepper, and D.B.Janssen (1999).
Thermodynamic analysis of halide binding to haloalkane dehalogenase suggests the occurrence of large conformational changes.
  Protein Sci, 8, 355-360.  
9915834 Y.Bourne, P.Taylor, P.E.Bougis, and P.Marchot (1999).
Crystal structure of mouse acetylcholinesterase. A peripheral site-occluding loop in a tetrameric assembly.
  J Biol Chem, 274, 2963-2970.
PDB code: 1maa
9591683 S.Kim, and B.A.Barry (1998).
The protein environment surrounding tyrosyl radicals D. and Z. in photosystem II: a difference Fourier-transform infrared spectroscopic study.
  Biophys J, 74, 2588-2600.  
  9154902 M.Holmgren, P.L.Smith, and G.Yellen (1997).
Trapping of organic blockers by closing of voltage-dependent K+ channels: evidence for a trap door mechanism of activation gating.
  J Gen Physiol, 109, 527-535.  
9247273 Y.Liu, M.Holmgren, M.E.Jurman, and G.Yellen (1997).
Gated access to the pore of a voltage-dependent K+ channel.
  Neuron, 19, 175-184.  
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 codes are shown on the right.

 

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