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PDBsum entry 1umk

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Oxidoreductase PDB id
1umk
Jmol
Contents
Protein chain
271 a.a. *
Ligands
FAD
Waters ×753
* Residue conservation analysis
PDB id:
1umk
Name: Oxidoreductase
Title: The structure of human erythrocyte nadh-cytochrome b5 reductase
Structure: Nadh-cytochrome b5 reductase. Chain: a. Synonym: b5r. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.75Å     R-factor:   0.167     R-free:   0.207
Authors: S.Bando,T.Takano,T.Yubisui,K.Shirabe,M.Takeshita,C.Horii, A.Nakagawa
Key ref:
S.Bando et al. (2004). Structure of human erythrocyte NADH-cytochrome b5 reductase. Acta Crystallogr D Biol Crystallogr, 60, 1929-1934. PubMed id: 15502298 DOI: 10.1107/S0907444904020645
Date:
03-Oct-03     Release date:   02-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00387  (NB5R3_HUMAN) -  NADH-cytochrome b5 reductase 3
Seq:
Struc:
301 a.a.
271 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.6.2.2  - Cytochrome-b5 reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADH + 2 ferricytochrome b5 = NAD+ + H+ + 2 ferrocytochrome b5
NADH
+ 2 × ferricytochrome b5
= NAD(+)
+ H(+)
+ 2 × ferrocytochrome b5
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     small molecule metabolic process   12 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444904020645 Acta Crystallogr D Biol Crystallogr 60:1929-1934 (2004)
PubMed id: 15502298  
 
 
Structure of human erythrocyte NADH-cytochrome b5 reductase.
S.Bando, T.Takano, T.Yubisui, K.Shirabe, M.Takeshita, A.Nakagawa.
 
  ABSTRACT  
 
Erythrocyte NADH-cytochrome b(5) reductase reduces methaemoglobin to functional haemoglobin. In order to examine the function of the enzyme, the structure of NADH-cytochrome b(5) reductase from human erythrocytes has been determined and refined by X-ray crystallography. At 1.75 A resolution, the root-mean-square deviations (r.m.s.d.) from standard bond lengths and angles are 0.006 A and 1.03 degrees , respectively. The molecular structure was compared with those of rat NADH-cytochrome b(5) reductase and corn nitrate reductase. The human reductase resembles the rat reductase in overall structure as well as in many side chains. Nevertheless, there is a large main-chain shift from the human reductase to the rat reductase or the corn reductase caused by a single-residue replacement from proline to threonine. A model of the complex between cytochrome b(5) and the human reductase has been built and compared with that of the haem-containing domain of the nitrate reductase molecule. The interaction between cytochrome b(5) and the human reductase differs from that of the nitrate reductase because of differences in the amino-acid sequences. The structures around 15 mutation sites of the human reductase have been examined for the influence of residue substitutions using the program ROTAMER. Five mutations in the FAD-binding domain seem to be related to cytochrome b(5).
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Overview of the human b5R structure with residue numbers at the beginning and the end of the secondary structures. A ball-and-stick model of FAD is superposed on an `omit' electron-density map contoured at 0.8 [96][sigma] . The FAD-binding domain is in blue, the NADH-binding domain in red and the linker domain in green. This figure was drawn using MOLSCRIPT (Kraulis, 1991[97] [Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]-[98][bluearr.gif] ), BOBSCRIPT (Esnouf, 1997[99] [Esnouf, R. M. (1997). J. Mol. Graph. 15, 132-134.]-[100][bluearr.gif] ) and RASTER3D (Merritt & Bacon, 1997[101] [Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 276, 505-524.]-[102][bluearr.gif] ).
Figure 2.
Figure 2 Sequence alignment of human, rat, pig and steer b5R (Strittmatter et al., 1992[105] [Strittmatter, R., Kittler, J. M., Coghill, J. E. & Ozols, J. (1992). J. Biol. Chem. 267, 2519-2523.]-[106][bluearr.gif] ) and RNR. The RNR sequence is aligned based on the three-dimensional structures. The background colours indicate the secondary structures of human b5R: green for [107][beta] -strand, red for [108][alpha] -helix and white for loop. Cyan represents residues that are identical to human b5R and yellow represents residues that are non-homologous to human b5R. Orange rectangles indicate mutation sites of human b5R and magenta rectangles below RNR indicate residues that interact with cytochrome b[5] (Lu et al., 1995[109] [Lu, G., Lindqvist, Y., Schneider, G., Dwivedi, U. & Campbell, W. H. (1995). J. Mol. Biol. 248, 931-948.]-[110][bluearr.gif] ).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1929-1934) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18343696 E.Fermo, P.Bianchi, C.Vercellati, A.P.Marcello, M.Garatti, O.Marangoni, W.Barcellini, and A.Zanella (2008).
Recessive hereditary methemoglobinemia: two novel mutations in the NADH-cytochrome b5 reductase gene.
  Blood Cells Mol Dis, 41, 50-55.  
  17401193 S.Kim, M.Suga, K.Ogasahara, T.Ikegami, Y.Minami, T.Yubisui, and T.Tsukihara (2007).
Structure of Physarum polycephalum cytochrome b5 reductase at 1.56 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 274-279.
PDB code: 2eix
16795038 N.E.Ward, N.R.Pellis, S.A.Risin, and D.Risin (2006).
Gene expression alterations in activated human T-cells induced by modeled microgravity.
  J Cell Biochem, 99, 1187-1202.  
17227547 R.Kumar, J.G.Wallis, C.Skidmore, and J.Browse (2006).
A mutation in Arabidopsis cytochrome b5 reductase identified by high-throughput screening differentially affects hydroxylation and desaturation.
  Plant J, 48, 920-932.  
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.