PDBsum entry 2g3h

Transport protein

PDB id: 2g3h

Contents

Protein chain

153 a.a. *

Ligands

CYN-HEM

Metals

_CL ×2

_MG

Waters ×267

* Residue conservation analysis

PDB id:

2g3h

Name:

Transport protein

Title:

Cyanide binding and heme cavity conformational transitions in drosophila melanogaster hexa-coordinate hemoglobin

Structure:

Globin. Chain: a. Engineered: yes. Mutation: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: glob1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.40Å R-factor: 0.156 R-free: 0.188

Authors:

D.De Sanctis,P.Ascenzi,A.Bocedi,S.Dewilde,T.Burmester,T.Hankeln, L.Moens,M.Bolognesi

Key ref:

D.de Sanctis et al. (2006). Cyanide binding and heme cavity conformational transitions in Drosophila melanogaster hexacoordinate hemoglobin. Biochemistry, 45, 10054-10061. PubMed id: 16906763 DOI: 10.1021/bi060462a

Date:

20-Feb-06 Release date: 03-Oct-06

Protein chain

Q9VF15  (Q9VF15_DROME) -  GEO09476p1 from Drosophila melanogaster

Seq: 153 a.a.

Struc: 153 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.11.1.7 - peroxidase.
• Reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/bi060462a

Biochemistry 45:10054-10061 (2006)

PubMed id: 16906763

Cyanide binding and heme cavity conformational transitions in Drosophila melanogaster hexacoordinate hemoglobin.

D.de Sanctis, P.Ascenzi, A.Bocedi, S.Dewilde, T.Burmester, T.Hankeln, L.Moens, M.Bolognesi.

ABSTRACT

The reason for the presence of hemoglobin-like molecules in insects, such as Drosophila melanogaster, that live in fully aerobic environments has yet to be determined. Heme endogenous hexacoordination (where HisE7 and HisF8 axial ligands to the heme Fe atom are both provided by the protein) is a recently discovered mechanism proposed to modulate O(2) affinity in hemoglobins from different species. Previous results have shown that D. melanogaster hemoglobin 1 (product of the glob1 gene) displays heme endogenous hexacoordination in both the ferrous and ferric states. Here we present kinetic data characterizing the exogenous cyanide ligand binding process, and the three-dimensional structure (at 1.4 A resolution) of the ensuing cyano-met D. melanogaster hemoglobin. Comparison with the crystal structure of the endogenously hexacoordinated D. melanogaster hemoglobin shows that the transition to the cyano-met form is supported by conformational readjustment in the CD-D-E region of the protein, which removes HisE7 from the heme. The structural and functional features of D. melanogaster hemoglobin are examined in light of previous results achieved for human and mouse neuroglobins and for human cytoglobin, which display heme endogenous hexacoordination. The study shows that, despite the rather constant value for cyanide association rate constants for the ferric hemoproteins, different distal site conformational readjustments and/or heme sliding mechanisms are displayed by the known hexacoordinate hemoglobins as a result of exogenous ligand binding.