PDBsum entry 1gdi

Oxygen transport

PDB id

1gdi

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Contents

			Protein chain

					153 a.a. *

			Ligands

					HEM-CMO

			Waters ×153

* Residue conservation analysis

PDB id:

1gdi

Links

Name:

Oxygen transport

Title:

Crystal structure of ferric complexes of the yellow lupin leghemoglobin with isoquinoline at 1.8 angstroms resolution (russian)

Structure:

Leghemoglobin (carbonmonoxy). Chain: a. Engineered: yes

Source:

Lupinus luteus. Yellow lupine. Organism_taxid: 3873

Resolution:

1.80Å

R-factor:

0.183

Authors:

E.Harutyunyan,T.Safonova,I.Kuranova

Key ref:

E.H.Harutyunyan et al. (1996). The binding of carbon monoxide and nitric oxide to leghaemoglobin in comparison with other haemoglobins. J Mol Biol, 264, 152-161. PubMed id: 8950274

Date:

14-Sep-94

Release date:

27-Feb-95

PROCHECK

	Headers

	References

Protein chain

P02240 (LGB2_LUPLU) - Leghemoglobin-2 from Lupinus luteus

Seq: Struc:					154 a.a. 153 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.?

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

	J Mol Biol 264:152-161 (1996)
PubMed id: 8950274

The binding of carbon monoxide and nitric oxide to leghaemoglobin in comparison with other haemoglobins.
E.H.Harutyunyan, T.N.Safonova, I.P.Kuranova, A.N.Popov, A.V.Teplyakov, G.V.Obmolova, B.K.Valnshtein, G.G.Dodson, J.C.Wilson.

ABSTRACT

Haemoglobins have the ability to discriminate between oxygen and other diatomic molecules. To further understanding of this process the X-ray crystal structures of carbonmonoxy and nitrosyl-leghaemoglobin have been determined at 1.8 A resolution. The ligand geometry is discussed in detail and the controversial issue of bent versus linear carbon monoxide binding is addressed. The bond angle of 160 degrees for CO-leghaemoglobin is in conflict with recent spectroscopy results on myoglobin but is consistent with angles obtained for myoglobin X-ray crystal structures. In contrast to the numerous carbon monoxide studies, very little stereochemical information is available for the nitric oxide adduct of haemoglobin. This is provided by the X-ray structure of NO-leghaemoglobin, which conforms to expected geometry with an Fe-NO angle of 147 degrees and a lengthened iron-proximal histidine bond. Thus crystallographic evidence is given for the predicted weakening of this bond on the binding of nitric oxide.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18618695

L.Sael, D.La, B.Li, R.Rustamov, and D.Kihara (2008).
Rapid comparison of properties on protein surface.

Proteins, 73, 1.

16941901

E.Baudouin, L.Pieuchot, G.Engler, N.Pauly, and A.Puppo (2006).
Nitric oxide is formed in Medicago truncatula-Sinorhizobium meliloti functional nodules.

Mol Plant Microbe Interact, 19, 970-975.

15942729

A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2005).
NO binding to naphthalene dioxygenase.

J Biol Inorg Chem, 10, 483-489.

PDB codes:

1uuv 1uuw

15744461

D.Pozzi, G.Amiconi, A.Arcovito, M.Girasole, and A.C.Castellano (2005).
Haem conformation of amphibian nytrosylhaemoglobins detected by XANES spectroscopy.

Eur Phys J E Soft Matter, 16, 373-379.

15258136

S.Galijasevic, G.M.Saed, M.P.Diamond, and H.M.Abu-Soud (2004).
High dissociation rate constant of ferrous-dioxy complex linked to the catalase-like activity in lactoperoxidase.

J Biol Chem, 279, 39465-39470.

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

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

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.

11352753

J.T.Trent, A.N.Hvitved, and M.S.Hargrove (2001).
A model for ligand binding to hexacoordinate hemoglobins.

Biochemistry, 40, 6155-6163.

11114067

C.Jung (2000).
Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy.

J Mol Recognit, 13, 325-351.

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

10681518

H.M.Abu-Soud, and S.L.Hazen (2000).
Nitric oxide modulates the catalytic activity of myeloperoxidase.

J Biol Chem, 275, 5425-5430.

10671516

H.Shimizu, E.Obayashi, Y.Gomi, H.Arakawa, S.Y.Park, H.Nakamura, S.Adachi, H.Shoun, and Y.Shiro (2000).
Proton delivery in NO reduction by fungal nitric-oxide reductase. Cryogenic crystallography, spectroscopy, and kinetics of ferric-NO complexes of wild-type and mutant enzymes.

J Biol Chem, 275, 4816-4826.

PDB codes:

1cl6 1cmj 1cmn

10986467

M.S.Hargrove, E.A.Brucker, B.Stec, G.Sarath, R.Arredondo-Peter, R.V.Klucas, J.S.Olson, and G.N.Phillips (2000).
Crystal structure of a nonsymbiotic plant hemoglobin.

Structure, 8, 1005-1014.

PDB code:

1d8u

10600110

A.M.Rich, P.J.Ellis, L.Tennant, P.E.Wright, R.S.Armstrong, and P.A.Lay (1999).
Determination of Fe-ligand bond lengths and the Fe-N-O bond angles in soybean ferrous and ferric nitrosylleghemoglobin a using multiple-scattering XAFS analyses.

Biochemistry, 38, 16491-16499.

9626580

C.Mathieu, S.Moreau, P.Frendo, A.Puppo, and M.J.Davies (1998).
Direct detection of radicals in intact soybean nodules: presence of nitric oxide-leghemoglobin complexes.

Free Radic Biol Med, 24, 1242-1249.

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

9586994

S.Nagashima, M.Nakasako, N.Dohmae, M.Tsujimura, K.Takio, M.Odaka, M.Yohda, N.Kamiya, and I.Endo (1998).
Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.

Nat Struct Biol, 5, 347-351.

PDB code:

2ahj

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.