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PDBsum entry 1iby
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protein ligands metals Protein-protein interface(s) links
Metal binding protein PDB id
1iby

 

 

 

 

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Contents
Protein chains
112 a.a. *
Ligands
HEZ ×4
Metals
_CU ×4
Waters ×581
* Residue conservation analysis
PDB id:
1iby
Name: Metal binding protein
Title: Red copper protein nitrosocyanin from nitrosomonas europaea
Structure: Nitrosocyanin. Chain: a, b, c, d
Source: Nitrosomonas europaea. Organism_taxid: 915
Biol. unit: Trimer (from PDB file)
Resolution:
1.65Å     R-factor:   0.186     R-free:   0.216
Authors: R.L.Lieberman,D.M.Arciero,A.B.Hooper,A.C.Rosenzweig
Key ref:
R.L.Lieberman et al. (2001). Crystal structure of a novel red copper protein from Nitrosomonas europaea. Biochemistry, 40, 5674-5681. PubMed id: 11341832 DOI: 10.1021/bi0102611
Date:
29-Mar-01     Release date:   06-Jun-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q820S6  (Q820S6_NITEU) -  Chain A, Red Copper Protein Nitrosocyanin from Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)
Seq:
Struc: 		136 a.a.
112 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/bi0102611 Biochemistry 40:5674-5681 (2001)
PubMed id: 11341832  
 
 
Crystal structure of a novel red copper protein from Nitrosomonas europaea.
R.L.Lieberman, D.M.Arciero, A.B.Hooper, A.C.Rosenzweig.
 
  ABSTRACT  
 
Nitrosocyanin (NC) is a mononuclear red copper protein isolated from the ammonia oxidizing bacterium Nitrosomonas europaea. Although NC exhibits some sequence homology to classic blue copper proteins, its spectroscopic and electrochemical properties are drastically different. The 1.65 A resolution crystal structure of oxidized NC reveals an unprecedented trimer of single domain cupredoxins. Each copper center is partially covered by an unusual extended beta-hairpin structure from an adjacent monomer. The copper ion is coordinated by His 98, His 103, Cys 95, a single side chain oxygen of Glu 60, and a solvent molecule. In the 2.3 A resolution structure of reduced NC, His 98 shifts away from the copper ion, and the solvent molecule is not observed. The arrangement of these ligands renders the coordination geometry of the NC red copper center distinct from that of blue copper centers. In particular, the red copper center has a higher coordination number and lacks the long Cu-S(Met) and short Cu-S(Cys) bond distances characteristic of blue copper. Moreover, the red copper center is square pyramidal whereas blue copper is typically distorted tetrahedral. Analysis of the NC structure provides insight into possible functions of this new type of biological copper center.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153850 S.M.Berry, E.L.Bladholm, E.J.Mostad, and A.R.Schenewerk (2011).
Incorporation of the red copper nitrosocyanin binding loop into blue copper azurin.
  J Biol Inorg Chem, 16, 473-480.  
20232870 G.S.Siluvai, M.Mayfield, M.J.Nilges, S.Debeer George, and N.J.Blackburn (2010).
Anatomy of a red copper center: spectroscopic identification and reactivity of the copper centers of Bacillus subtilis Sco and its Cys-to-Ala variants.
  J Am Chem Soc, 132, 5215-5226.  
20169379 M.G.Savelieff, and Y.Lu (2010).
Cu(A) centers and their biosynthetic models in azurin.
  J Biol Inorg Chem, 15, 461-483.  
19921776 G.S.Siluvai, M.M.Nakano, M.Mayfield, M.J.Nilges, and N.J.Blackburn (2009).
H135A controls the redox activity of the Sco copper center. Kinetic and spectroscopic studies of the His135Ala variant of Bacillus subtilis Sco.
  Biochemistry, 48, 12133-12144.  
19299503 K.Sato, C.Li, I.Salard, A.J.Thompson, M.J.Banfield, and C.Dennison (2009).
Metal-binding loop length and not sequence dictates structure.
  Proc Natl Acad Sci U S A, 106, 5616-5621.
PDB codes: 3fs9 3fsa 3fsv 3fsw 3fsz 3ft0
18535143 M.G.Savelieff, T.D.Wilson, Y.Elias, M.J.Nilges, D.K.Garner, and Y.Lu (2008).
Experimental evidence for a link among cupredoxins: red, blue, and purple copper transformations in nitrous oxide reductase.
  Proc Natl Acad Sci U S A, 105, 7919-7924.  
16091356 Y.C.Horng, S.C.Leary, P.A.Cobine, F.B.Young, G.N.George, E.A.Shoubridge, and D.R.Winge (2005).
Human Sco1 and Sco2 function as copper-binding proteins.
  J Biol Chem, 280, 34113-34122.  
12949080 F.Arnesano, L.Banci, M.Benvenuti, I.Bertini, V.Calderone, S.Mangani, and M.S.Viezzoli (2003).
The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction.
  J Biol Chem, 278, 45999-46006.
PDB codes: 1naq 1osc
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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