PDBsum entry 1jzk

Oxygen storage/transport

PDB id

1jzk

Loading ...

Contents

			Protein chains

					145 a.a. *

			Ligands

					HEM ×4

			Waters ×228

* Residue conservation analysis

PDB id:

1jzk

Links

Name:

Oxygen storage/transport

Title:

Crystal structure of scapharca inaequivalvis hbi, i114f mutant (deoxy)

Structure:

Globin i - ark shell. Chain: a, b, c, d. Synonym: dimeric hemoglobin, hbi. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å

R-factor:

0.179

R-free:

0.214

Authors:

J.E.Knapp,Q.H.Gibson,L.Cushing,W.E.Royer Jr.

Key ref:

J.E.Knapp et al. (2001). Restricting the ligand-linked heme movement in Scapharca dimeric hemoglobin reveals tight coupling between distal and proximal contributions to cooperativity. Biochemistry, 40, 14795-14805. PubMed id: 11732898 DOI: 10.1021/bi011071t

Date:

16-Sep-01

Release date:

19-Dec-01

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)

DOI no: 10.1021/bi011071t	Biochemistry 40:14795-14805 (2001)
PubMed id: 11732898

Restricting the ligand-linked heme movement in Scapharca dimeric hemoglobin reveals tight coupling between distal and proximal contributions to cooperativity.
J.E.Knapp, Q.H.Gibson, L.Cushing, W.E.Royer.

ABSTRACT

Cooperative ligand binding in the dimeric hemoglobin from the blood clam Scapharca inaequivalvis results primarily from tertiary, rather than quaternary, structural changes. Ligand binding is coupled with conformational changes of key residues, including Phe 97, which is extruded from the proximal heme pocket, and the heme group, which moves deeper into the heme pocket. We have tested the role of the heme movement in cooperative function by mutating Ile 114, at the base of the heme pocket. Replacement of this residue with a Met did not disturb the hemoglobin structure or significantly alter equilibrium ligand binding properties. In contrast, substitution with a Phe at position 114 inhibits the ligand-linked movement of the heme group, and substantially reduces oxygen affinity and cooperativity. As the extent of heme movement to the normal position of the ligated state is diminished, Phe 97 is inhibited from its movement into the interface upon ligand binding. These results indicate a tight coupling between these two key cooperative transitions and suggest that the heme movement may be an obligatory trigger for expulsion of Phe 97 from the heme pocket.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20963788

X.Wang, W.Zhao, X.Lin, B.Su, and J.Liu (2010).
Observation of symmetric denaturation of hemoglobin subunits by electrospray ionization mass spectrometry.

J Mass Spectrom, 45, 1306-1311.

18380000

C.Ciaccio, A.Coletta, G.De Sanctis, S.Marini, and M.Coletta (2008).
Cooperativity and allostery in haemoglobin function.

IUBMB Life, 60, 112-123.

18398907

N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, and K.Miki (2008).
Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins.

Proteins, 73, 113-125.

PDB code:

2zfo

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

16684887

J.E.Knapp, R.Pahl, V.Srajer, and W.E.Royer (2006).
Allosteric action in real time: time-resolved crystallographic studies of a cooperative dimeric hemoglobin.

Proc Natl Acad Sci U S A, 103, 7649-7654.

PDB codes:

2grf 2grh 2grz

15932877

W.E.Royer, H.Zhu, T.A.Gorr, J.F.Flores, and J.E.Knapp (2005).
Allosteric hemoglobin assembly: diversity and similarity.

J Biol Chem, 280, 27477-27480.

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.