PDBsum entry 6iyh

Oxygen binding/transport protein

PDB id: 6iyh

Contents

Protein chains

142 a.a.

145 a.a.

Ligands

HEM ×2

PGO

Waters ×388

PDB id:

6iyh

Name:

Oxygen binding/transport protein

Title:

X-ray sequence and high resolution crystal structure of persian sturgeon methemoglobin

Structure:

Alpha chain. Chain: a. Other_details: sequence is derived from structure. Beta chain. Chain: b. Other_details: sequence derived from structure

Source:

Acipenser persicus. Organism_taxid: 61968. Organism_taxid: 61968

Resolution:

1.70Å R-factor: 0.160 R-free: 0.196

Authors:

A.Seyedarabi

Key ref:

A.Seyedarabi et al. (2019). Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation. Biochim Biophys Acta Proteins Proteom, 1867, 586-594. PubMed id: 30904680 DOI: 10.1016/j.bbapap.2019.03.008

Date:

16-Dec-18 Release date: 10-Apr-19

Supersedes:

5jgg

Protein chain

A0A1X8XL85  (A0A1X8XL85_ACIPE) -  Alpha chain from Acipenser persicus

Seq: 142 a.a.

Struc: 142 a.a.*

Protein chain

A0A1X8XL86  (A0A1X8XL86_ACIPE) -  Beta chain from Acipenser persicus

Seq: 146 a.a.

Struc: 145 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

DOI no: 10.1016/j.bbapap.2019.03.008

Biochim Biophys Acta Proteins Proteom 1867:586-594 (2019)

PubMed id: 30904680

Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation.

A.Seyedarabi, S.Ariaeenejad, A.A.Moosavi-Movahedi, S.Rayati, N.Poursasan, N.Asiaie, Z.Seraj, F.Mehraban, S.E.Seyedarabi.

ABSTRACT

Although there is a high sequence similarity between mammalian and fish hemoglobin (Hb), the oxidation and heme loss rates can vary greatly between them such that fish Hbs oxidise much more rapidly than mammalian Hbs. There is to date no sequence or structural data for any sturgeon Hb to reveal the level of autoxidation in these fish. In this study, novel high resolution X-ray sequences and crystal structures of methemoglobin (Met-Hb) from two sturgeon fish including Persian sturgeon (Acipenser percisus) and Starry sturgeon (Acipenser stellatus) belonging to the Caspian sea has been determined. A comprehensive sequence and structure comparison between these sturgeon Met-Hbs and a number of non-sturgeon and normal and sickle cell anaemia human Hb in varying heme states has been carried out highlighting (i) the structural variability in the heme propionate groups; (ii) the existence of certain residues or their displacement and shift in the heme pocket allowing entry of water molecules into the heme pocket; (iii) the importance of the number of water molecules in the heme pocket; (iv) the hydrogen bonding between oxygens of A and D propionate groups and that of waters in the heme pocket; and (v) the role of heme binding waters causing oxidative stress and heme autoxidation.