PDBsum entry 2blh

Oxygen transport

PDB id

2blh

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Contents

			Protein chain

					153 a.a. *

			Ligands

					HEM

			Waters ×131

* Residue conservation analysis

PDB id:

2blh

Links

Name:

Oxygen transport

Title:

Ligand migration and protein fluctuations in myoglobin mutant l29w

Structure:

Myoglobin. Chain: a. Engineered: yes. Mutation: yes. Other_details: slow co rebinder

Source:

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

Resolution:

1.77Å

R-factor:

0.187

R-free:

0.202

Authors:

K.Nienhaus,A.Ostermann,G.U.Nienhaus,F.G.Parak,M.Schmidt

Key ref:

K.Nienhaus et al. (2005). Ligand migration and protein fluctuations in myoglobin mutant L29W. Biochemistry, 44, 5095-5105. PubMed id: 15794647 DOI: 10.1021/bi047513t

Date:

04-Mar-05

Release date:

06-Apr-05

PROCHECK

	Headers

	References

Protein chain

P02185 (MYG_PHYMC) - Myoglobin from Physeter macrocephalus

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]

DOI no: 10.1021/bi047513t	Biochemistry 44:5095-5105 (2005)
PubMed id: 15794647

Ligand migration and protein fluctuations in myoglobin mutant L29W.
K.Nienhaus, A.Ostermann, G.U.Nienhaus, F.G.Parak, M.Schmidt.

ABSTRACT

We have determined eight X-ray structures of myoglobin mutant L29W at various experimental conditions. In addition, infrared spectroscopic experiments are presented, which are discussed in the light of the X-ray structures. Two distinct conformations of the CO-ligated protein were identified, giving rise to two stretching bands of heme-bound CO. If L29W MbCO crystals are illuminated around 180 K, a deoxy species is formed. The CO molecules migrate to the proximal side of the heme and remain trapped in the so-called Xe1 cavity upon temperature decrease to 105 K. The structure of this photoproduct is almost identical to the equilibrium high-temperature deoxy Mb structure. If the temperature is cycled to increasingly higher values, CO recombination is observed. Three intermediate structures have been determined during the rebinding process. Efficient recombination occurs only above 180 K, the characteristic temperature for the onset of protein dynamics. Rebinding is remarkably slow because bulky residues His64 and Trp29 block important migration pathways of the CO molecule.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21445845

K.Nienhaus, E.Nickel, C.Lu, S.R.Yeh, and G.U.Nienhaus (2011).
Ligand migration in human indoleamine-2,3 dioxygenase.

IUBMB Life, 63, 153-159.

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.

19655795

R.A.Goldbeck, M.L.Pillsbury, R.A.Jensen, J.L.Mendoza, R.L.Nguyen, J.S.Olson, J.Soman, D.S.Kliger, and R.M.Esquerra (2009).
Optical detection of disordered water within a protein cavity.

J Am Chem Soc, 131, 12265-12272.

PDB codes:

3h57 3h58

17975837

A.D.Nadra, M.A.Martí, A.Pesce, M.Bolognesi, and D.A.Estrin (2008).
Exploring the molecular basis of heme coordination in human neuroglobin.

Proteins, 71, 695-705.

18840607

M.D.Salter, K.Nienhaus, G.U.Nienhaus, S.Dewilde, L.Moens, A.Pesce, M.Nardini, M.Bolognesi, and J.S.Olson (2008).
The apolar channel in Cerebratulus lacteus hemoglobin is the route for O2 entry and exit.

J Biol Chem, 283, 35689-35702.

PDB codes:

2vyy 2vyz

17905436

Z.N.Zahran, L.Chooback, D.M.Copeland, A.H.West, and G.B.Richter-Addo (2008).
Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations.

J Inorg Biochem, 102, 216-233.

PDB codes:

2o58 2o5b 2o5l 2o5m 2o5o 2o5q 2o5s 2o5t

18001141

K.Nienhaus, J.E.Knapp, P.Palladino, W.E.Royer, and G.U.Nienhaus (2007).
Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.

Biochemistry, 46, 14018-14031.

PDB codes:

2r4w 2r4x 2r4y 2r4z 2z85 2z8a

17959373

T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.

Curr Opin Struct Biol, 17, 580-586.

16547137

D.Bourgeois, B.Vallone, A.Arcovito, G.Sciara, F.Schotte, P.A.Anfinrud, and M.Brunori (2006).
Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography.

Proc Natl Acad Sci U S A, 103, 4924-4929.

16129597

D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.

Curr Opin Struct Biol, 15, 538-547.

16085709

M.Schmidt, K.Nienhaus, R.Pahl, A.Krasselt, S.Anderson, F.Parak, G.U.Nienhaus, and V.Srajer (2005).
Ligand migration pathway and protein dynamics in myoglobin: a time-resolved crystallographic study on L29W MbCO.

Proc Natl Acad Sci U S A, 102, 11704-11709.

PDB codes:

2bw9 2bwh

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.