PDBsum entry 1a4a

Electron transport

PDB id: 1a4a

Contents

Protein chains

129 a.a. *

Metals

_CU ×2

Waters ×657

* Residue conservation analysis

PDB id:

1a4a

Name:

Electron transport

Title:

Azurin mutant with met 121 replaced by his, ph 6.5 crystal form, data collected at 16 degrees celsius

Structure:

Azurin. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Achromobacter denitrificans. Organism_taxid: 32002. Cellular_location: periplasm. Gene: azu. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.89Å R-factor: 0.189

Authors:

A.Messerschmidt,L.Prade

Key ref:

A.Messerschmidt et al. (1998). Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH. Proc Natl Acad Sci U S A, 95, 3443-3448. PubMed id: 9520385 DOI: 10.1073/pnas.95.7.3443

Date:

28-Jan-98 Release date: 29-Apr-98

Protein chains

P00280  (AZUR_ACHDE) -  Azurin from Achromobacter denitrificans

Seq: 149 a.a.

Struc: 129 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DOI no: 10.1073/pnas.95.7.3443

Proc Natl Acad Sci U S A 95:3443-3448 (1998)

PubMed id: 9520385

Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH.

A.Messerschmidt, L.Prade, S.J.Kroes, J.Sanders-Loehr, R.Huber, G.W.Canters.

ABSTRACT

The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyramidal structure imposed by the protein with three strong equatorial ligands (one Cys and two His) provides a favorable geometry for both cuprous and cupric oxidation states. However, the crystal structures of the Met121His mutant of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal binding cavity in the protein is more flexible than expected. At high pH (6.5), the Cu site retains the same three equatorial ligands as in the wild-type azurin and adds His121 as a fourth strong ligand, creating a tetrahedral copper site geometry with a green color referred to as 1.5 type. In the low pH (3.5) structure, the protonation of His121 causes a conformational change in residues 117-123, moving His121 away from the copper. The empty coordination site is occupied by an oxygen atom of a nitrate molecule of the buffer solution. This axial ligand is coordinated less strongly, generating a distorted tetrahedral copper geometry with a blue color and spectroscopic properties of a type-1 site. These crystal structures demonstrate that blue copper proteins are flexible enough to permit a range of movement of the Cu atom along the axial direction of the trigonal pyramid.

Selected figure(s)

Figure 1.
Fig. 1. Copper site of A. denitrificans Met121His azurin. (A) High pH form. The indicated distances are the mean values over the subunits in HP1 and HP2. (B) Low pH form. The displayed distances are the mean values between subunits C and D of LP. Image produced with SETOR (24).

Figure 3.
Fig. 3. Overlay of the low pH form (subunit D of LP, blue) onto high pH form (subunit A of LP, green) of the copper sites and the polypeptide stretch 120-124. The included 2.45-Å resolution F[o]-F[c] omit electron density map was calculated with residues 120-123, and nitrate in subunits D was removed and running a 200-cycle positional refinement before map calculation. The map has been contoured at 3.0 . Image produced with SETOR (24).

Figures were selected by an automated process.