PDBsum entry 1jdo

Oxygen transport

PDB id

1jdo

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Contents

			Protein chain

					154 a.a. *

			Ligands

					SO4


					HEM-_NO

			Waters ×138

* Residue conservation analysis

PDB id:

1jdo

Links

Name:

Oxygen transport

Title:

Sperm whale myoglobin (ferrous, nitric oxide bound)

Structure:

Myoglobin. Chain: a. Engineered: yes. Mutation: yes

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PQS)

Resolution:

1.90Å

R-factor:

0.155

R-free:

0.206

Authors:

E.A.Brucker,G.N.Phillips Jr.

Key ref:

E.A.Brucker et al. (1998). Nitric oxide myoglobin: crystal structure and analysis of ligand geometry. Proteins, 30, 352-356. PubMed id: 9533619

Date:

10-Feb-98

Release date:

27-May-98

PROCHECK

	Headers

	References

Protein chain

P02185 (MYG_PHYMC) - Myoglobin from Physeter macrocephalus

Seq: Struc:					154 a.a. 155 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class 2:

E.C.1.11.1.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 3:

E.C.1.7.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

	Proteins 30:352-356 (1998)
PubMed id: 9533619

Nitric oxide myoglobin: crystal structure and analysis of ligand geometry.
E.A.Brucker, J.S.Olson, M.Ikeda-Saito, G.N.Phillips.

ABSTRACT

The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 angstroms resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112 degrees. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the N(epsilon) atom of histidine64 is located 2.8 angstroms away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20218710

A.V.Soldatova, M.Ibrahim, J.S.Olson, R.S.Czernuszewicz, and T.G.Spiro (2010).
New light on NO bonding in Fe(III) heme proteins from resonance raman spectroscopy and DFT modeling.

J Am Chem Soc, 132, 4614-4625.

19161328

N.J.Silvernail, A.Barabanschikov, J.T.Sage, B.C.Noll, and W.R.Scheidt (2009).
Mapping NO movements in crystalline [Fe(Porph)(NO)(1-MeIm)].

J Am Chem Soc, 131, 2131-2140.

17925395

L.Thijs, E.Vinck, A.Bolli, F.Trandafir, X.Wan, D.Hoogewijs, M.Coletta, A.Fago, R.E.Weber, S.Van Doorslaer, P.Ascenzi, M.Alam, L.Moens, and S.Dewilde (2007).
Characterization of a globin-coupled oxygen sensor with a gene-regulating function.

J Biol Chem, 282, 37325-37340.

17534533

P.Moënne-Loccoz (2007).
Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins.

Nat Prod Rep, 24, 610-620.

17177434

M.Ibrahim, C.Xu, and T.G.Spiro (2006).
Differential sensing of protein influences by NO and CO vibrations in heme adducts.

J Am Chem Soc, 128, 16834-16845.

16476730

M.Negrerie, S.G.Kruglik, J.C.Lambry, M.H.Vos, J.L.Martin, and S.Franzen (2006).
Role of heme iron coordination and protein structure in the dynamics and geminate rebinding of nitric oxide to the H93G myoglobin mutant: implications for nitric oxide sensors.

J Biol Chem, 281, 10389-10398.

16774917

Y.Gao, S.F.El-Mashtoly, B.Pal, T.Hayashi, K.Harada, and T.Kitagawa (2006).
Pathway of information transmission from heme to protein upon ligand binding/dissociation in myoglobin revealed by UV resonance raman spectroscopy.

J Biol Chem, 281, 24637-24646.

16089422

W.Zeng, N.J.Silvernail, D.C.Wharton, G.Y.Georgiev, B.M.Leu, W.R.Scheidt, J.Zhao, W.Sturhahn, E.E.Alp, and J.T.Sage (2005).
Direct probe of iron vibrations elucidates NO activation of heme proteins.

J Am Chem Soc, 127, 11200-11201.

14517970

D.M.Copeland, A.H.West, and G.B.Richter-Addo (2003).
Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane.

Proteins, 53, 182-192.

PDB codes:

1npf 1npg

14645054

D.R.Nutt, and M.Meuwly (2003).
Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin.

Biophys J, 85, 3612-3623.

12819228

J.Friedman, L.Lad, R.Deshmukh, H.Li, A.Wilks, and T.L.Poulos (2003).
Crystal structures of the NO- and CO-bound heme oxygenase from Neisseriae meningitidis. Implications for O2 activation.

J Biol Chem, 278, 34654-34659.

PDB codes:

1p3t 1p3u 1p3v

12480932

S.Van Doorslaer, S.Dewilde, L.Kiger, S.V.Nistor, E.Goovaerts, M.C.Marden, and L.Moens (2003).
Nitric oxide binding properties of neuroglobin. A characterization by EPR and flash photolysis.

J Biol Chem, 278, 4919-4925.

12146965

S.Nagatomo, M.Nagai, N.Shibayama, and T.Kitagawa (2002).
Differences in changes of the alpha1-beta2 subunit contacts between ligand binding to the alpha and beta subunits of hemoglobin A: UV resonance raman analysis using Ni-Fe hybrid hemoglobin.

Biochemistry, 41, 10010-10020.

10821858

D.Leys, K.Backers, T.E.Meyer, W.R.Hagen, M.A.Cusanovich, and J.J.Van Beeumen (2000).
Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.

J Biol Chem, 275, 16050-16056.

PDB codes:

1dw0 1dw1 1dw2 1dw3

11060017

D.M.Lawson, C.E.Stevenson, C.R.Andrew, and R.R.Eady (2000).
Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase.

EMBO J, 19, 5661-5671.

PDB codes:

1e83 1e84 1e85 1e86

9760233

D.Nurizzo, F.Cutruzzolà, M.Arese, D.Bourgeois, M.Brunori, C.Cambillau, and M.Tegoni (1998).
Conformational changes occurring upon reduction and NO binding in nitrite reductase from Pseudomonas aeruginosa.

Biochemistry, 37, 13987-13996.

PDB codes:

1bl9 1nno

9843411

N.L.Chan, P.H.Rogers, and A.Arnone (1998).
Crystal structure of the S-nitroso form of liganded human hemoglobin.

Biochemistry, 37, 16459-16464.

PDB code:

1buw

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.