PDBsum entry 1ndh

Electron transport (flavo protein)

PDB id

1ndh

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Contents

			Protein chain

					270 a.a. *

			Ligands

					FAD

			Waters ×48

* Residue conservation analysis

PDB id:

1ndh

Links

Name:

Electron transport (flavo protein)

Title:

Crystal structure of nadh-cytochrome b5 reductase from pig liver at 2.4 angstroms resolution

Structure:

Cytochrome b5 reductase. Chain: a. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823

Resolution:

2.10Å

R-factor:

0.223

Authors:

H.Nishida,K.Miki

Key ref:

H.Nishida et al. (1995). Crystal structure of NADH-cytochrome b5 reductase from pig liver at 2.4 A resolution. Biochemistry, 34, 2763-2767. PubMed id: 7893687 DOI: 10.1021/bi00009a004

Date:

31-Oct-94

Release date:

14-Feb-95

PROCHECK

	Headers

	References

Protein chain

P83686 (NB5R3_PIG) - NADH-cytochrome b5 reductase 3 (Fragment) from Sus scrofa

Seq: Struc:					272 a.a. 270 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:

2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD⁺ + H⁺

2 × Fe(III)-[cytochrome b5]	+	NADH	=	2 × Fe(II)-[cytochrome b5]	+	NAD(+)	+	H(+)

Cofactor:

FAD

FAD
Bound ligand (Het Group name = FAD) corresponds exactly

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi00009a004	Biochemistry 34:2763-2767 (1995)
PubMed id: 7893687

Crystal structure of NADH-cytochrome b5 reductase from pig liver at 2.4 A resolution.
H.Nishida, K.Inaka, M.Yamanaka, S.Kaida, K.Kobayashi, K.Miki.

ABSTRACT

The three-dimensional structure of NADH-cytochrome b5 reductase from pig liver microsomes has been determined at 2.4 A resolution by X-ray crystallography. The molecular structure reveals two domains, the FAD binding domain and the NADH domain. A large cleft lies between these two domains and contains the binding site for the FAD prosthetic group. The backbone structure of the FAD binding domain has a great similarity to that of ferredoxin-NADP+ reductase [Karplus, P. A., Daniels, M. J., & Herriott, J. R. (1991) Science 251, 60-65], in spite of the relatively low sequence homology (about 15%) between the two enzymes. On the other hand, the structure of the NADH domain has several structural differences from that of the NADP+ domain of ferredoxin-NADP+ reductase. The size of the cleft between the two domains is larger in NADH-cytochrome b5 reductase than in ferredoxin-NADP+ reductase, which may be responsible for the observed difference in the nucleotide accessibility in the two enzymes.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18279389

M.A.Musumeci, A.K.Arakaki, D.V.Rial, D.L.Catalano-Dupuy, and E.A.Ceccarelli (2008).
Modulation of the enzymatic efficiency of ferredoxin-NADP(H) reductase by the amino acid volume around the catalytic site.

FEBS J, 275, 1350-1366.

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

17341833

T.Ikegami, E.Kameyama, S.Y.Yamamoto, Y.Minami, and T.Yubisui (2007).
Structure and properties of the recombinant NADH-cytochrome b5 reductase of Physarum polycephalum.

Biosci Biotechnol Biochem, 71, 783-790.

15603910

M.J.Percy, N.V.McFerran, and T.R.Lappin (2005).
Disorders of oxidised haemoglobin.

Blood Rev, 19, 61-68.

15502298

S.Bando, T.Takano, T.Yubisui, K.Shirabe, M.Takeshita, and A.Nakagawa (2004).
Structure of human erythrocyte NADH-cytochrome b5 reductase.

Acta Crystallogr D Biol Crystallogr, 60, 1929-1934.

PDB code:

1umk

12756024

D.Grabowska, D.Plochocka, E.Jablonska-Skwiecinska, A.Chelstowska, I.Lewandowska, K.Staniszewska, Z.Majewska, I.Witos, and B.Burzynska (2003).
Compound heterozygosity of two missense mutations in the NADH-cytochrome b5 reductase gene of a Polish patient with type I recessive congenital methaemoglobinaemia.

Eur J Haematol, 70, 404-409.

12829278

I.Schröder, E.Johnson, and S.de Vries (2003).
Microbial ferric iron reductases.

FEMS Microbiol Rev, 27, 427-447.

12459552

S.Kimura, M.Kawamura, and T.Iyanagi (2003).
Role of Thr(66) in porcine NADH-cytochrome b5 reductase in catalysis and control of the rate-limiting step in electron transfer.

J Biol Chem, 278, 3580-3589.

11525168

H.J.Chiu, E.Johnson, I.Schröder, and D.C.Rees (2001).
Crystal structures of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP+.

Structure, 9, 311-319.

PDB codes:

1i0r 1i0s

11514662

O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.

Protein Sci, 10, 1712-1728.

11106776

D.F.Lewis, and P.Hlavica (2000).
Interactions between redox partners in various cytochrome P450 systems: functional and structural aspects.

Biochim Biophys Acta, 1460, 353-374.

10998235

G.A.Ziegler, and G.E.Schulz (2000).
Crystal structures of adrenodoxin reductase in complex with NADP+ and NADPH suggesting a mechanism for the electron transfer of an enzyme family.

Biochemistry, 39, 10986-10995.

PDB codes:

1e1k 1e1l 1e1m 1e1n

11188687

P.Rowland, S.Nørager, K.F.Jensen, and S.Larsen (2000).
Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.

Structure, 8, 1227-1238.

PDB codes:

1ep1 1ep2 1ep3

10353815

M.Ingelman, S.Ramaswamy, V.Nivière, M.Fontecave, and H.Eklund (1999).
Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli.

Biochemistry, 38, 7040-7049.

PDB code:

1qfj

10082957

S.Kimura, Y.Emi, S.Ikushiro, and T.Iyanagi (1999).
Systematic mutations of highly conserved His49 and carboxyl-terminal of recombinant porcine liver NADH-cytochrome b5 reductase solubilized domain.

Biochim Biophys Acta, 1430, 290-301.

15012211

W.H.Campbell (1999).
NITRATE REDUCTASE STRUCTURE, FUNCTION AND REGULATION: Bridging the Gap between Biochemistry and Physiology.

Annu Rev Plant Physiol Plant Mol Biol, 50, 277-303.

9865948

G.Sridhar Prasad, N.Kresge, A.B.Muhlberg, A.Shaw, Y.S.Jung, B.K.Burgess, and C.D.Stout (1998).
The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii.

Protein Sci, 7, 2541-2549.

PDB code:

1a8p

9718311

V.Nivière, M.A.Vanoni, G.Zanetti, and M.Fontecave (1998).
Reaction of the NAD(P)H:flavin oxidoreductase from Escherichia coli with NADPH and riboflavin: identification of intermediates.

Biochemistry, 37, 11879-11887.

9115439

C.Tarricone, A.Galizzi, A.Coda, P.Ascenzi, and M.Bolognesi (1997).
Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp.

Structure, 5, 497-507.

PDB codes:

1vhb 2vhb

9237990

M.Wang, D.L.Roberts, R.Paschke, T.M.Shea, B.S.Masters, and J.J.Kim (1997).
Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes.

Proc Natl Acad Sci U S A, 94, 8411-8416.

PDB code:

1amo

8880927

H.Nishida, and K.Miki (1996).
Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: pyridine nucleotide-binding and interaction with an electron-transfer partner.

Proteins, 26, 32-41.

8663185

V.Nivière, F.Fieschi, J.L.Décout, and M.Fontecave (1996).
Is the NAD(P)H:flavin oxidoreductase from Escherichia coli a member of the ferredoxin-NADP+ reductase family?. Evidence for the catalytic role of serine 49 residue.

J Biol Chem, 271, 16656-16661.

8557026

U.Ermler, R.A.Siddiqui, R.Cramm, and B.Friedrich (1995).
Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.

EMBO J, 14, 6067-6077.

PDB code:

1cqx

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.