PDBsum entry: 1ik6

Oxidoreductase

PDB-id: 1ik6

Asymmetric unit

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PROCHECK

Protein chain

284 a.a. *

Waters ×134

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, tetramer
- as defined in PDB file (see also PQS)

PDB id:

1ik6

Name:

Oxidoreductase

Title:

3d structure of the e1beta subunit of pyruvate dehydrogenase from the archeon pyrobaculum aerophilum

Structure:

Pyruvate dehydrogenase. Chain: a. Fragment: e1beta subunit. Engineered: yes

Source:

Pyrobaculum aerophilum. Organism_taxid: 13773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biological unit:

Tetramer (from PDB file)

UniProt:

Q8ZUR7 (Q8ZUR7_PYRAE)

Seq:

Struc:

Seq:

320 a.a.

Struc:

284 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Resolution:

2.00Å

R-factor:

0.212

R-free:

0.255

Authors:

G.Kleiger,J.Perry,D.Eisenberg

Key ref:

G.Kleiger et al. (2001). 3D structure and significance of the GPhiXXG helix packing motif in tetramers of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum.. Biochemistry, 40, 14484-14492. [PubMed id: 11724561] [DOI: 10.1021/bi011016k]

Date:

02-May-01

Release date:

19-Dec-01

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Clefts

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Key reference

DOI no: 10.1021/bi011016k

Biochemistry 40:14484-14492 (2001)

PubMed id: 11724561

3D structure and significance of the GPhiXXG helix packing motif in tetramers of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum.

G.Kleiger, J.Perry, D.Eisenberg.

ABSTRACT

As part of a structural genomics project, we have determined the 2.0 A structure of the E1beta subunit of pyruvate dehydrogenase from Pyrobaculum aerophilum (PA), a thermophilic archaeon. The overall fold of E1beta from PA is closely similar to the previously determined E1beta structures from humans (HU) and P. putida (PP). However, unlike the HU and PP structures, the PA structure was determined in the absence of its partner subunit, E1alpha. Significant structural rearrangements occur in E1beta when its E1alpha partner is absent, including rearrangement of several secondary structure elements such as helix C. Helix C is buried by E1alpha in the HU and PP structures, but makes crystal contacts in the PA structure that lead to an apparent beta(4) tetramer. Static light scattering and sedimentation velocity data are consistent with the formation of PA E1beta tetramers in solution. The interaction of helix C with its symmetry-related counterpart stabilizes the tetrameric interface, where two glycine residues on the same face of one helix create a packing surface for the other helix. This GPhiXXG helix-helix interaction motif has previously been found in interacting transmembrane helices, and is found here at the E1alpha-E1beta interface for both the HU and PP alpha(2)beta(2) tetramers. As a case study in structural genomics, this work illustrates that comparative analysis of protein structures can identify the structural significance of a sequence motif.