4B3W

Crystal structure of human cytoglobin H(E7)Q mutant

Summary for 4B3W

• Entry DOI: 10.2210/pdb4b3w/pdb
• Related: 1UMO 1URV 1URY 1UT0 1UX9 1V5H 2DC3
• Descriptor: CYTOGLOBIN, PROTOPORPHYRIN IX CONTAINING FE, CYANIDE ION, ... (6 entities in total)
• Functional Keywords: oxygen transport, metal binding protein, heme hexacoordination, protein cavity
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Cytoplasm (By similarity): Q8WWM9
• Total number of polymer chains: 2
• Total formula weight: 44550.88

Authors

Gabba, M.,Abbruzzetti, S.,Spyrakis, F.,Forti, F.,Bruno, S.,Mozzarelli, A.,Luque, F.J.,Viappiani, C.,Cozzini, P.,Nardini, M.,Germani, F.,Bolognesi, M.,Moens, L.,Dewilde, S. (deposition date: 2012-07-26, release date: 2013-01-23, Last modification date: 2023-12-20)

Primary citation

Gabba, M.,Abbruzzetti, S.,Spyrakis, F.,Forti, F.,Bruno, S.,Mozzarelli, A.,Luque, F.J.,Viappiani, C.,Cozzini, P.,Nardini, M.,Germani, F.,Bolognesi, M.,Moens, L.,Dewilde, S.
Co Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin.
Plos One, 8:49770-, 2013

PubMed Abstract: Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein.

PubMed: 23308092
DOI: 10.1371/JOURNAL.PONE.0049770

Experimental method

X-RAY DIFFRACTION (2.8 Å)