PDBsum entry 2r4x

Oxygen binding

PDB id

2r4x

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Contents

			Protein chains

					145 a.a. *

			Ligands

					HEM-CMO ×2

			Waters ×98

* Residue conservation analysis

PDB id:

2r4x

Links

Name:

Oxygen binding

Title:

Ligand migration and binding in the dimeric hemoglobin of scapharca inaequivalvis: h69v/i114m co complex

Structure:

Globin-1. Chain: a, b. Synonym: globin i, hbi, dimeric hemoglobin. Engineered: yes. Mutation: yes

Source:

Scapharca inaequivalvis. Ark clam. Organism_taxid: 6561. Gene: hbi. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å

R-factor:

0.186

R-free:

0.210

Authors:

J.E.Knapp,W.E.Royer Jr.,K.Nienhaus,P.Palladino,G.U.Nienhaus

Key ref:

K.Nienhaus et al. (2007). Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis. Biochemistry, 46, 14018-14031. PubMed id: 18001141

Date:

02-Sep-07

Release date:

27-Nov-07

PROCHECK

	Headers

	References

Protein chains

P02213 (GLB1_ANAIN) - Globin-1 from Anadara inaequivalvis

Seq: Struc:					146 a.a. 145 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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

	Biochemistry 46:14018-14031 (2007)
PubMed id: 18001141

Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.
K.Nienhaus, J.E.Knapp, P.Palladino, W.E.Royer, G.U.Nienhaus.

ABSTRACT

Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19913476

D.Bourgeois (2009).
Watching CO enmeshed in hemoglobin.

Structure, 17, 1427-1428.

19767648

E.Nickel, K.Nienhaus, C.Lu, S.R.Yeh, and G.U.Nienhaus (2009).
Ligand and substrate migration in human indoleamine 2,3-dioxygenase.

J Biol Chem, 284, 31548-31554.

19913484

J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, and W.E.Royer (2009).
Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.

Structure, 17, 1494-1504.

PDB codes:

3g46 3g4q 3g4r 3g4u 3g4v 3g4w 3g4y 3g52 3g53

18839332

J.W.Murray, K.Maghlaoui, J.Kargul, M.Sugiura, and J.Barber (2008).
Analysis of xenon binding to photosystem II by X-ray crystallography.

Photosynth Res, 98, 523-527.

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.