PDBsum entry 2e2e

Lyase

PDB id: 2e2e

Contents

Protein chains

171 a.a. *

Ligands

BME ×2

IMD ×2

Waters ×190

* Residue conservation analysis

PDB id:

2e2e

Name:

Lyase

Title:

Tpr domain of nrfg mediates the complex formation between heme lyase and formate-dependent nitrite reductase in escherichia coli o157:h7

Structure:

Formate-dependent nitrite reductase complex nrfg subunit. Chain: a, b. Fragment: tetratricopeptide repeat motif. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: o157 : h7 edl933. Gene: nrfg. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.05Å R-factor: 0.235 R-free: 0.268

Authors:

D.Han,K.Kim,J.Oh,J.Park,Y.Kim

Key ref:

D.Han et al. (2008). TPR domain of NrfG mediates complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia coli O157:H7. Proteins, 70, 900-914. PubMed id: 17803240 DOI: 10.1002/prot.21597

Date:

11-Nov-06 Release date: 23-Oct-07

Protein chains

Q8X5S3  (NRFG_ECO57) -  Formate-dependent nitrite reductase complex subunit NrfG from Escherichia coli O157:H7

Seq: 198 a.a.

Struc: 171 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1002/prot.21597

Proteins 70:900-914 (2008)

PubMed id: 17803240

TPR domain of NrfG mediates complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia coli O157:H7.

D.Han, K.Kim, J.Oh, J.Park, Y.Kim.

ABSTRACT

Escherichia coli synthesize C-type cytochromes only during anaerobic growth in media supplemented with nitrate and nitrite. The reduction of nitrate to ammonium in the periplasm of Escherichia coli involves two separate periplasmic enzymes, nitrate reductase and nitrite reductase. The nitrite reductase involved, NrfA, contains cytochrome C and is synthesized coordinately with a membrane-associated cytochrome C, NrfB, during growth in the presence of nitrite or in limiting nitrate concentrations. The genes NrfE, NrfF, and NrfG are required for the formate-dependent nitrite reduction pathway, which involves at least two C-type cytochrome proteins, NrfA and NrfB. The NrfE, NrfF, and NrfG genes (heme lyase complex) are involved in the maturation of a special C-type cytochrome, apocytochrome C (apoNrfA), to cytochrome C (NrfA) by transferring a heme to the unusual heme binding motif of the Cys-Trp-Ser-Cys-Lys sequence in apoNrfA protein. Thus, in order to further investigate the roles of NrfG in the formation of heme lyase complex (NrfEFG) and in the interaction between heme lyase complex and formate-dependent nitrite reductase (NrfA), we determined the crystal structure of NrfG at 2.05 A. The structure of NrfG showed that the contact between heme lyase complex (NrfEFG) and NrfA is accomplished via a TPR domain in NrfG which serves as a binding site for the C-terminal motif of NrfA. The portion of NrfA that binds to TPR domain of NrfG has a unique secondary motif, a helix followed by about a six-residue C-terminal loop (the so called "hook conformation"). This study allows us to better understand the mechanism of special C-type cytochrome assembly during the maturation of formate-dependent nitrite reductase, and also adds a new TPR binding conformation to the list of TPR-mediated protein-protein interactions.

Selected figure(s)

Figure 5.
Figure 5. Interactions of inter-TPR turns among homologous TPR domains. Interactions between adjacent TPR units are mediated by hydrogen bonding between Pro (position 32, i) and Trp (position 4 in the next helix, i+6). Proline at position 32 is generally highly conserved for this purpose. Therefore, the position 4 is generally occupied by Trp, Tyr, and His.[34] A detailed view of an inter-TPR turn is shown and is representative of several TPR domains. (A) Inter-TPR turn of CTPR3[34] and the turn1 of NrfG. In CTPR3, the backbone carbonyl of Pro74 interacts with the side-chain nitrogen of Trp80. In NrfG, the backbone carbonyl of Pro70 interacts with the side-chain nitrogen of Trp76. (B) Inter-TPR turns of NrFG. Although Pro at position 32 of the turn 2 and 4 is substituted by Gly104 and Ser176, respectively, Tyr110 and Arg181 interact with Gly110 and Ser176, respectively, to stabilize the turns. (C) Inter-TPR turn with no hydrogen bond. Interestingly, Leu320 (OGT) and Leu147 (NrfG) are placed at position i+6 and thus they cannot form hydrogen binds in the turns of OGT and NrfG. The turn between TPR9 and TPR10 in OGT is -142°, whereas that of turn3 between TPR2 and TPR3 of NrfG is -139°, which are both lower angles than the packing angles of other TPR domains with hydrogen bonds at the turns (also see Table II).

Figure 9.
Figure 9. Conformational differences among concave TPR grooves in TPR domains. To compare conformation and their binding residues in TPR domains, the NrfG structure (orange) was superimposed onto the corresponding CHIP (green) and HOP TPR1 (purple helices) with RMSDs of 2.31 Å and 2.07 Å, respectively. The corresponding bound residues in the compared TPR domains are represented in ball-and-stick fashion. These comparisons show that the highly conserved Asn and Lys residues in HOP and CHIP are mainly substituted by hydrophobic residues (Ala, Leu) in NrfG. (A) The residues Glu81, Ala112, Tyr119, and Thr145 of NrfG correspond to Asn 35, Asn 66, Lys 73, Lys96 of CHIP [noted in the Fig. 5(A)], the residues of which are shown. (B) The residues Ala77, Glu81, Ala112, Tyr119, Thr145, and Leu149 of NrfG correspond to Lys8, Asn12, Asn43, Lys50, Lys73, and Arg77 of HOP TPR1 [noted in the Fig. 5(B)], the residues of which are shown.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 900-914) copyright 2008.

Figures were selected by an automated process.