PDBsum entry 1vrf

Heme protein

PDB id: 1vrf

Contents

Protein chain

147 a.a. *

Ligands

HEM-CMO

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Solution structure and backbone dynamics of component IV glycera dibranchiata monomeric hemoglobin-Co.
• Authors: B.F.Volkman, S.L.Alam, J.D.Satterlee, J.L.Markley.
• Ref.: Biochemistry, 1998, 37, 10906-10919. [DOI no: 10.1021/bi980810b]
• PubMed id: 9692983

Abstract

The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87.

Secondary reference #1

• Title: Detailed nmr analysis of the heme-Protein interactions in component IV glycera dibranchiata monomeric hemoglobin-Co.
• Authors: S.L.Alam, B.F.Volkman, J.L.Markley, J.D.Satterlee.
• Ref.: J Biomol Nmr, 1998, 11, 119-133.
• PubMed id: 9679291