Novel β-Barrel Fold in the Nuclear Magnetic Resonance Structure of the Replicase Nonstructural Protein 1 from the Severe Acute Respiratory Syndrome Coronavirus

ABSTRACT The nonstructural protein 1 (nsp1) of the severe acute respiratory syndrome coronavirus has 179 residues and is the N-terminal cleavage product of the viral replicase polyprotein that mediates RNA replication and processing. The specific function of nsp1 is not known. Here we report the nuclear magnetic resonance structure of the nsp1 segment from residue 13 to 128, which represents a novel α/β-fold formed by a mixed parallel/antiparallel six-stranded β-barrel, an α-helix covering one opening of the barrel, and a 310-helix alongside the barrel. We further characterized the full-length 179-residue protein and show that the polypeptide segments of residues 1 to 12 and 129 to 179 are flexibly disordered. The structure is analyzed in a search for possible correlations with the recently reported activity of nsp1 in the degradation of mRNA.

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Nuclear Magnetic Resonance Structure of the N-Terminal Domain of Nonstructural Protein 3 from the Severe Acute Respiratory Syndrome Coronavirus

Journal of Virology ◽

10.1128/jvi.00969-07 ◽

2007 ◽

Vol 81 (21) ◽

pp. 12049-12060 ◽

Cited By ~ 48

Author(s):

Pedro Serrano ◽

Margaret A. Johnson ◽

Marcius S. Almeida ◽

Reto Horst ◽

Torsten Herrmann ◽

...

Keyword(s):

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Severe Acute Respiratory Syndrome ◽

Nonstructural Protein ◽

Resonance Structure ◽

Nuclear Magnetic Resonance Structure ◽

Globular Domain ◽

Terminal Domain ◽

Nonstructural Protein 3 ◽

Nuclear Magnetic

ABSTRACT This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four β-strands and two α-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.

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Nuclear Magnetic Resonance Structure Shows that the Severe Acute Respiratory Syndrome Coronavirus-Unique Domain Contains a Macrodomain Fold

Journal of Virology ◽

10.1128/jvi.01781-08 ◽

2008 ◽

Vol 83 (4) ◽

pp. 1823-1836 ◽

Cited By ~ 33

Author(s):

Amarnath Chatterjee ◽

Margaret A. Johnson ◽

Pedro Serrano ◽

Bill Pedrini ◽

Jeremiah S. Joseph ◽

...

Keyword(s):

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Severe Acute Respiratory Syndrome ◽

Three Dimensional ◽

Dimensional Structure ◽

Resonance Structure ◽

Nuclear Magnetic Resonance Structure ◽

Three Dimensional Structure ◽

Unique Domain ◽

Nuclear Magnetic

ABSTRACT The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for “middle of the SARS-unique domain”) in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

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The CheZ Binding Interface of CheAS Is Located in α-Helix E

Journal of Bacteriology ◽

10.1128/jb.00294-09 ◽

2009 ◽

Vol 191 (18) ◽

pp. 5845-5848 ◽

Cited By ~ 6

Author(s):

Christopher O'Connor ◽

Philip Matsumura ◽

Andres Campos

Keyword(s):

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Resonance Structure ◽

Nuclear Magnetic Resonance Structure ◽

Binding Interface ◽

Α Helix ◽

Interaction Surface ◽

Nuclear Magnetic

ABSTRACT Specific CheA-short (CheAS) residues, L123 and L126, were identified as critical for CheZ binding. In the CheAS ′P1-CheZ nuclear magnetic resonance structure, these residues form an interaction surface on α-helix E in the ′P1 domain. Both L123 and L126 are buried in CheA-long (CheAL), providing an explanation for why CheAL fails to bind CheZ.

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