Home LiteratureArticle Details
PMID: 16498413 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Structural and functional insights into the B30.2/SPRY domain.

The EMBO journal ·Vol. 25 ·No. 6 ·2006-03-22 ·Pages 1353-63

Woo JS, Imm JH, Min CK, Kim KJ, Cha SS, Oh BH

Abstract

The B30.2/SPRY domain is present in approximately 700 eukaryotic (approximately 150 human) proteins, including medically important proteins such as TRIM5alpha and Pyrin. Nonetheless, the functional role of this modular domain remained unclear. Here, we report the crystal structure of an SPRY-SOCS box family protein GUSTAVUS in complex with Elongins B and C, revealing a highly distorted two-layered beta-sandwich core structure of its B30.2/SPRY domain. Ensuing studies identified one end of the beta-sandwich as the surface interacting with an RNA helicase VASA with a 40 nM dissociation constant. The sequence variation in TRIM5alpha responsible for HIV-1 restriction and most of the mutations in Pyrin causing familial Mediterranean fever map on this surface, implicating the corresponding region in many B30.2/SPRY domains as the ligand-binding site. The amino acids lining the binding surface are highly variable among the B30.2/SPRY domains, suggesting that these domains are protein-interacting modules, which recognize a specific individual partner protein rather than a consensus sequence motif.

MeSH Terms
Amino Acid Motifs Amino Acid Sequence Animals Binding Sites Carrier Proteins/chemistry,genetics Cytoskeletal Proteins/chemistry DEAD-box RNA Helicases Drosophila Proteins/chemistry,genetics,metabolism Elongin Ligands Models, Molecular Molecular Sequence Data Mutation/genetics Protein Binding Protein Conformation Protein Folding Protein Structure, Tertiary Pyrin RNA Helicases/genetics,metabolism Sequence Homology, Amino Acid Transcription Factors/chemistry,genetics
Chemicals
Carrier Proteins Cytoskeletal Proteins Drosophila Proteins Elongin Ligands MEFV protein, human Pyrin Transcription Factors gus protein, Drosophila vas protein, Drosophila DEAD-box RNA Helicases RNA Helicases
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Woo Jae-Sung
Division of Molecular and Life Sciences, Department of Life Sciences, Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea.
Imm Joon-Hyuk
Min Chang-Ki
Kim Kyung-Jin
Cha Sun-Shin
Oh Byung-Ha
References (48)
48 references, click to expand
  1. Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function.
    Science. 1999 Apr 16;284(5413):455-61 PMID: 10205047
  2. High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution.
    Structure. 1999 Oct 15;7(10):1223-33 PMID: 10545323
  3. VASA mediates translation through interaction with a Drosophila yIF2 homolog.
    Mol Cell. 2000 Jan;5(1):181-7 PMID: 10678180
  4. The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms.
    Mol Cell. 2000 Nov;6(5):1169-82 PMID: 11106755
  5. Episodic evolution of pyrin in primates: human mutations recapitulate ancestral amino acid states.
    Nat Genet. 2001 Mar;27(3):318-21 PMID: 11242116
  6. InterProScan--an integration platform for the signature-recognition methods in InterPro.
    Bioinformatics. 2001 Sep;17(9):847-8 PMID: 11590104
  7. The 52 000 MW Ro/SS-A autoantigen in Sjögren's syndrome/systemic lupus erythematosus (Ro52) is an interferon-gamma inducible tripartite motif protein associated with membrane proximal structures.
    Immunology. 2002 Jun;106(2):246-56 PMID: 12047754
  8. Activation of Ras/Erk pathway by a novel MET-interacting protein RanBPM.
    J Biol Chem. 2002 Sep 27;277(39):36216-22 PMID: 12147692
  9. VASA localization requires the SPRY-domain and SOCS-box containing protein, GUSTAVUS.
    Dev Cell. 2002 Dec;3(6):865-76 PMID: 12479811
  10. The MID1/PP2A complex: a key to the pathogenesis of Opitz BBB/G syndrome.
    Bioessays. 2003 Apr;25(4):356-66 PMID: 12655643
  11. A tripartite motif protein TRIM11 binds and destabilizes Humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults.
    Eur J Neurosci. 2003 Mar;17(6):1150-8 PMID: 12670303
  12. X-linked Opitz syndrome: novel mutations in the MID1 gene and redefinition of the clinical spectrum.
    Am J Med Genet A. 2003 Jul 15;120A(2):222-8 PMID: 12833403
  13. Familial Mediterranean fever.
    Pediatr Nephrol. 2003 Sep;18(9):853-9 PMID: 12836090
  14. Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides.
    Nature. 1992 Aug 20;358(6388):646-53 PMID: 1379696
  15. A novel zinc finger coiled-coil domain in a family of nuclear proteins.
    Trends Biochem Sci. 1992 Sep;17(9):344-5 PMID: 1412709
  16. The Pfam protein families database.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41 PMID: 14681378
  17. Structure-function analysis of GNIP, the glycogenin-interacting protein.
    Arch Biochem Biophys. 2004 Jan 15;421(2):236-42 PMID: 14984203
  18. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys.
    Nature. 2004 Feb 26;427(6977):848-53 PMID: 14985764
  19. Cullin-based ubiquitin ligases: Cul3-BTB complexes join the family.
    EMBO J. 2004 Apr 21;23(8):1681-7 PMID: 15071497
  20. A single amino acid change in the SPRY domain of human Trim5alpha leads to HIV-1 restriction.
    Curr Biol. 2005 Jan 11;15(1):73-8 PMID: 15649369
  21. Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain.
    Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2832-7 PMID: 15689398
  22. Species-specific variation in the B30.2(SPRY) domain of TRIM5alpha determines the potency of human immunodeficiency virus restriction.
    J Virol. 2005 Mar;79(5):3139-45 PMID: 15709033
  23. Retrovirus restriction by TRIM5alpha variants from Old World and New World primates.
    J Virol. 2005 Apr;79(7):3930-7 PMID: 15767395
  24. Highly efficient protein expression and purification using bacterial hemoglobin fusion vector.
    Plasmid. 2005 May;53(3):274-82 PMID: 15848232
  25. TRIM family proteins: retroviral restriction and antiviral defence.
    Nat Rev Microbiol. 2005 Oct;3(10):799-808 PMID: 16175175
  26. Retroviral restriction factor TRIM5alpha is a trimer.
    J Virol. 2005 Nov;79(22):14446-50 PMID: 16254380
  27. Relationship between SPRY and B30.2 protein domains. Evolution of a component of immune defence?
    Immunology. 2005 Dec;116(4):411-7 PMID: 16313355
  28. Improved methods for building protein models in electron density maps and the location of errors in these models.
    Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9 PMID: 2025413
  29. Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-26 PMID: 27754618
  30. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides.
    Nat Struct Biol. 1994 Aug;1(8):546-51 PMID: 7664083
  31. SCOP: a structural classification of proteins database for the investigation of sequences and structures.
    J Mol Biol. 1995 Apr 7;247(4):536-40 PMID: 7723011
  32. Evolutionary study of multigenic families mapping close to the human MHC class I region.
    J Mol Evol. 1993 Dec;37(6):600-12 PMID: 8114113
  33. Carboxy-terminal cytoplasmic domain of mouse butyrophilin specifically associates with a 150-kDa protein of mammary epithelial cells and milk fat globule membrane.
    Biochim Biophys Acta. 1995 Dec 14;1245(3):285-92 PMID: 8541302
  34. Interactions of protein antigens with antibodies.
    Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):7-12 PMID: 8552677
  35. Dali: a network tool for protein structure comparison.
    Trends Biochem Sci. 1995 Nov;20(11):478-80 PMID: 8578593
  36. Analyses of carbohydrate recognition by legume lectins: size of the combining site loops and their primary specificity.
    J Mol Biol. 1997 Mar 28;267(2):433-45 PMID: 9096236
  37. A family of cytokine-inducible inhibitors of signalling.
    Nature. 1997 Jun 26;387(6636):917-21 PMID: 9202125
  38. SPRY domains in ryanodine receptors (Ca(2+)-release channels).
    Trends Biochem Sci. 1997 Jun;22(6):193-4 PMID: 9204703
  39. Ancient missense mutations in a new member of the RoRet gene family are likely to cause familial Mediterranean fever. The International FMF Consortium.
    Cell. 1997 Aug 22;90(4):797-807 PMID: 9288758
  40. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
    Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 PMID: 9396791
  41. Twenty proteins containing a C-terminal SOCS box form five structural classes.
    Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):114-9 PMID: 9419338
  42. Protein structure prediction. Implications for the biologist.
    Biochimie. 1997 Nov;79(11):681-6 PMID: 9479451
  43. X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution.
    J Biol Chem. 1998 May 22;273(21):13047-52 PMID: 9582341
  44. SMART, a simple modular architecture research tool: identification of signaling domains.
    Proc Natl Acad Sci U S A. 1998 May 26;95(11):5857-64 PMID: 9600884
  45. Crystallography & NMR system: A new software suite for macromolecular structure determination.
    Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21 PMID: 9757107
  46. B30.2-like domain proteins: update and new insights into a rapidly expanding family of proteins.
    Mol Biol Evol. 1998 Dec;15(12):1696-705 PMID: 9866204
  47. The Elongin BC complex interacts with the conserved SOCS-box motif present in members of the SOCS, ras, WD-40 repeat, and ankyrin repeat families.
    Genes Dev. 1998 Dec 15;12(24):3872-81 PMID: 9869640
  48. JPred: a consensus secondary structure prediction server.
    Bioinformatics. 1998;14(10):892-3 PMID: 9927721
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1038/sj.emboj.7600994
Published
2006-03-22
Epub
2006-00-23
Pages
1353-63
Language
English
Region
England
NLM ID
8208664
PMCID
PMC1422157
Subset
IM
Databases
GENBANK
AAA17031, AAB64200, AAH10861, CAH72715
PDB
1A3K, 1C1L, 1MZ5, 1OQ1, 1UAI, 1UPS, 1UX6, 1YIF
RefSeq
NP_000234, NP_001723, NP_003189, NP_003736, NP_006360, NP_056441, NP_057198, NP_065901, NP_079382, NP_149023, NP_150632, NP_477514, NP_724402, XP_117294
External Links
PubMed source DOI: 10.1038/sj.emboj.7600994 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2