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PDBsum entry 1t5k
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protein ligands metals Protein-protein interface(s) links
Electron transport PDB id
1t5k

 

 

 

 

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Contents
Protein chains
105 a.a. *
Ligands
PO4 ×5
Metals
_CO ×4
Waters ×617
* Residue conservation analysis
PDB id:
1t5k
Name: Electron transport
Title: Crystal structure of amicyanin substituted with cobalt
Structure: Amicyanin. Chain: a, b, c, d. Engineered: yes
Source: Paracoccus denitrificans. Organism_taxid: 266. Gene: mauc, ami. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.40Å     R-factor:   0.184     R-free:   0.210
Authors: C.J.Carrell,X.Wang,L.Jones,W.L.Jarrett,V.L.Davidson,F.S.Mathews
Key ref:
C.J.Carrell et al. (2004). Crystallographic and NMR investigation of cobalt-substituted amicyanin. Biochemistry, 43, 9381-9389. PubMed id: 15260481 DOI: 10.1021/bi049635r
Date:
04-May-04     Release date:   27-Jul-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22364  (AMCY_PARDE) -  Amicyanin from Paracoccus denitrificans
Seq:
Struc: 		131 a.a.
105 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi049635r Biochemistry 43:9381-9389 (2004)
PubMed id: 15260481  
 
 
Crystallographic and NMR investigation of cobalt-substituted amicyanin.
C.J.Carrell, X.Wang, L.Jones, W.L.Jarrett, V.L.Davidson, F.S.Mathews.
 
  ABSTRACT  
 
Cobalt(II) amicyanin was prepared by replacing the copper of the type I copper protein amicyanin from Paracoccus denitrificans with cobalt. The structure of the protein and the metal center have been characterized by X-ray crystallography and paramagnetic NMR spectroscopy. The crystal structure indicates that Met98, which provides an axial sulfur ligand in native amicyanin, is no longer bound to the metal in cobalt(II) amicyanin and that a water molecule is recruited from solvent to form the fourth metal ligand. This results in a tetrahedral coordination geometry for the cobalt ion. NMR studies in solution also indicate that the side chain of the methionine residue interacts less strongly with the metal in P. denitrificans amicyanin than in Paracoccus versutus amicyanin. The cobalt(II) amicyanin crystal structure is different from that of cobalt-substituted azurin in which the carbonyl of a glycine residue provides this equivalent ligand. In cobalt(II) amicyanin that residue is a proline, for which the oxygen is structurally inaccessible, so that the water occupies the position held by the glycine carbonyl in cobalt(II) azurin. Such a metal coordination involving water has not previously been reported for a native or metal-substituted type I copper protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21258692 M.Choi, and V.L.Davidson (2011).
Cupredoxins--a study of how proteins may evolve to use metals for bioenergetic processes.
  Metallomics, 3, 140-151.  
20945335 R.Gessmann, C.Kyvelidou, M.Papadovasilaki, and K.Petratos (2011).
The crystal structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis.
  Biopolymers, 95, 202-207.
PDB code: 3nyk
19639146 S.Sottini, G.Mathies, P.Gast, D.Maganas, P.Kyritsis, and E.J.Groenen (2009).
A W-band pulsed EPR/ENDOR study of Co(II)S(4) coordination in the Co[(SPPh(2))(SP(i)Pr(2))N](2) complex.
  Phys Chem Chem Phys, 11, 6727-6732.  
17986390 J.K.Ma, S.Lee, M.Choi, G.R.Bishop, J.P.Hosler, and V.L.Davidson (2008).
The axial ligand and extent of protein folding determine whether Zn or Cu binds to amicyanin.
  J Inorg Biochem, 102, 342-346.  
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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