2JZD

NMR structure of the domain 527-651 of the SARS-CoV nonstructural protein nsp3

Summary for 2JZD

• Entry DOI: 10.2210/pdb2jzd/pdb
• Related: 2JZE 2JZF 2RNK
• NMR Information: BMRB: 15618
• Descriptor: Replicase polyprotein 1ab (1 entity in total)
• Functional Keywords: sars-cov, sars-unique domain, nonstructural protein, nsp3, nsp3c, functional and structural proteomics of sars-cov-related proteins, fsps, psi-2, protein structure initiative, joint center for structural genomics, jcsg, atp-binding, cytoplasm, endonuclease, exonuclease, helicase, hydrolase, membrane, metal-binding, nuclease, nucleotide-binding, nucleotidyltransferase, protease, ribosomal frameshift, rna replication, rna-binding, rna-directed rna polymerase, thiol protease, transferase, transmembrane, zinc, zinc-finger, viral protein
• Biological source: SARS coronavirus
• Cellular location: Non-structural protein 3: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 4: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 6: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 7: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 8: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 9: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 10: Host cytoplasm, host perinuclear region (By similarity). Helicase: Host endoplasmic reticulum-Golgi intermediate compartment (Potential). Uridylate-specific endoribonuclease: Host cytoplasm, host perinuclear region (By similarity): P59641
• Total number of polymer chains: 1
• Total formula weight: 14366.68

Authors

Chatterjee, A.,Johnson, M.A.,Serrano, P.,Pedrini, B.,Joseph, J.,Saikatendu, K.,Neuman, B.,Stevens, R.C.,Wilson, I.A.,Buchmeier, M.J.,Kuhn, P.,Wuthrich, K.,Joint Center for Structural Genomics (JCSG) (deposition date: 2008-01-04, release date: 2008-02-05, Last modification date: 2024-05-29)

Primary citation

Chatterjee, A.,Johnson, M.A.,Serrano, P.,Pedrini, B.,Joseph, J.S.,Neuman, B.W.,Saikatendu, K.,Buchmeier, M.J.,Kuhn, P.,Wuthrich, K.
Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.
J.Virol., 83:1823-1836, 2009

PubMed 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.

PubMed: 19052085
DOI: 10.1128/JVI.01781-08

Experimental method

SOLUTION NMR