메뉴 건너뛰기




Volumn 6, Issue 3, 1996, Pages 386-394

Structural classification of proteins: New superfamilies

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; DOUBLE STRANDED RNA; FLAVOPROTEIN; LIGASE; MACROPHAGE MIGRATION INHIBITION FACTOR; PROTEASOME;

EID: 0029950031     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80059-5     Document Type: Article
Times cited : (231)

References (49)
  • 1
    • 13444266385 scopus 로고
    • Protein architecture: New superfamilies
    • Murzin AG, Chothia C: Protein architecture: new superfamilies. Curr Opin Struct Biol 1 992, 2:895-903.
    • (1992) Curr Opin Struct Biol , vol.2 , pp. 895-903
    • Murzin, A.G.1    Chothia, C.2
  • 2
    • 0027918455 scopus 로고
    • New folds for all-β proteins
    • Chothia C, Murzin AG: New folds for all-β proteins. Structure 1993, 1:217-222.
    • (1993) Structure , vol.1 , pp. 217-222
    • Chothia, C.1    Murzin, A.G.2
  • 4
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540. The SCOP database organizes protein structures hierarchically, identifying likely evolutionary relationships. It complements information on structural similarity provided by other databases. SCOP is available on the internet at URL: http://scop.mrc-lmb.cam.ac.uk/scop/.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 5
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • Chothia C: One thousand families for the molecular biologist Nature 1992, 387:543-544.
    • (1992) Nature , vol.387 , pp. 543-544
    • Chothia, C.1
  • 6
    • 0028593509 scopus 로고
    • Protein super-families and domain superfolds
    • Orengo CA, Jones DT, Thornton JM: Protein super-families and domain superfolds. Nature 1994, 372:631-634. This paper describes the highlights of an automated clustering of the protein database by the SSAP program. More details can be found at URL: http://www.biochem.ucl.ac.uk/bsm/cath/.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 7
    • 0028871926 scopus 로고
    • Dali: A network tool for protein structure comparison
    • Holm L, Sander C: Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995, 20:478-480. This effective tool for detection of similarities to known structures in the PDB database has come to the internet (see URL: http://www.embl-heidelberg.de/dali/).
    • (1995) Trends Biochem Sci , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 8
    • 0029249826 scopus 로고
    • β-Glucosyltransferase and phosphorylase reveal their common theme
    • Artymiuk PJ, Rice DW, Poirrette AR, Willett P: β-Glucosyltransferase and phosphorylase reveal their common theme. Nat Struct Biol 1995, 2:11 7-120. See annotation [9••].
    • (1995) Nat Struct Biol , vol.2 , pp. 117-120
    • Artymiuk, P.J.1    Rice, D.W.2    Poirrette, A.R.3    Willett, P.4
  • 9
    • 0028969335 scopus 로고
    • Evolutionary link between glycogen phosphorylase and a DNa modifying enzyme
    • Holm L, Sander C: Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme. EMBO J 1995, 14:1287-1293. This paper, together with [8••] reports a striking structural similarity between a large protein and a very large protein detected by different computer algorithms: PROTEP for the former, and Dali for the latter. The similarity is so extensive that there is little doubt about the common evolutionary origin of the two enzymes, which also retain a functional similarity. The authors of [8••] are cautious in making this conclusion, however.
    • (1995) EMBO J , vol.14 , pp. 1287-1293
    • Holm, L.1    Sander, C.2
  • 10
    • 0029360327 scopus 로고
    • DNA polymerase β belongs to an ancient nucleotidyltransferase superfamily
    • Holm L, Sander C: DNA polymerase β belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci 1995, 20:345-347. On the basis of morphological similarities, DNA polymerase β was proposed to be distantly related to other DNA and RNA polymerases of known structure. This hypothesis is disproved here by the discovery of its true evolutionary relation.
    • (1995) Trends Biochem Sci , vol.20 , pp. 345-347
    • Holm, L.1    Sander, C.2
  • 11
    • 0029001623 scopus 로고
    • Crystal structure of DCoH, a bifunctional protein binding transcriptional coactivator
    • Endrizzi J, Cronk J, Wang W, Crabtree G, Alber T: Crystal structure of DCoH, a bifunctional protein binding transcriptional coactivator. Science 1995, 268:556-559.
    • (1995) Science , vol.268 , pp. 556-559
    • Endrizzi, J.1    Cronk, J.2    Wang, W.3    Crabtree, G.4    Alber, T.5
  • 12
    • 0028999219 scopus 로고
    • Three-dimensional structure of the bifunctional protein PCD/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1
    • Ficner R, Sauer UH, Stier G, Suck D: Three-dimensional structure of the bifunctional protein PCD/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1. EMBO J 1995, 14:2034-2042.
    • (1995) EMBO J , vol.14 , pp. 2034-2042
    • Ficner, R.1    Sauer, U.H.2    Stier, G.3    Suck, D.4
  • 13
    • 0028841677 scopus 로고
    • A potential catalytic site revealed by the 1.7 a crystal structure of the aminoterminal signalling domain of Sonic hedgehog
    • Hall TM, Porter JA, Beachy PA, Leahy DJ: A potential catalytic site revealed by the 1.7 A crystal structure of the aminoterminal signalling domain of Sonic hedgehog. Nature 1995, 378:212-216. The structure suggests the existence of potential hydrolytic activity in members of the hedgehog family, the primary signals expressed by certain embryonic patterning centres.
    • (1995) Nature , vol.378 , pp. 212-216
    • Hall, T.M.1    Porter, J.A.2    Beachy, P.A.3    Leahy, D.J.4
  • 14
    • 0028972449 scopus 로고
    • A protein catalytic framework with an N-terminal nucleophile is capable of self-activation
    • Brannigan JA, Dodson G, Duggleby HJ, Moody PCE, Smith JL, Tomchik DR, Murzin AG: A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 1995, 378:416-419. This paper describes a new superfamily of the Ntn hydrolases, which are characterized by the use of the side chain of the N-terminal amino acid as the nucleophile in catalysis. It also contains the prediction that glycosylas-paraginase belongs to this superfamily, which has been confirmed by the determination of its structure [36•].
    • (1995) Nature , vol.378 , pp. 416-419
    • Brannigan, J.A.1    Dodson, G.2    Duggleby, H.J.3    Moody, P.C.E.4    Smith, J.L.5    Tomchik, D.R.6    Murzin, A.G.7
  • 16
    • 0029971584 scopus 로고    scopus 로고
    • Crystal structure of the macrophage migration inhibitory factor from rat liver
    • Suzuki M, Sugimoto H, Nakagawa A, Tanaka I, Nishihira J, Sakai M: Crystal structure of the macrophage migration inhibitory factor from rat liver. Nat Struct Biol 1996, 3:259-266. The paper reports the unexpected structural similarity of MIF to CHMI, a tautomerase [18••]. This similarity extends to the putative active site regions, suggesting a possible enzymatic activity for this lymphokine.
    • (1996) Nat Struct Biol , vol.3 , pp. 259-266
    • Suzuki, M.1    Sugimoto, H.2    Nakagawa, A.3    Tanaka, I.4    Nishihira, J.5    Sakai, M.6
  • 17
  • 18
    • 0030060180 scopus 로고    scopus 로고
    • Enzymatic ketonization of 2-hydroxymuconate: Specificity and mechanism investigated by the crystal structures of two isomereases
    • Subramanya HS, Roper Dl, Dauter Z, Dodson EJ, Davies GJ, Wilson KS, Wigley DB: Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomereases. Biochemistry 1996, 35:792-802. This paper describes the crystal structures of two enzymes, CHMI and 4-OT, both of which catalyze the isomerization of unsaturated ketons. They have no significant sequence similarity, and the latter is only half the size of the former. Nevertheless, the CHMI monomer has a fold similar to that of the 4-OT dimer, and its trimer closely resembles the 4-OT hexamer.
    • (1996) Biochemistry , vol.35 , pp. 792-802
    • Subramanya, H.S.1    Roper, D.2    Dauter, Z.3    Dodson, E.J.4    Davies, G.J.5    Wilson, K.S.6    Wigley, D.B.7
  • 19
    • 0030593377 scopus 로고    scopus 로고
    • 1.6 Ȧ structure of nuclear transport factor 2 (NTF2)
    • in press
    • Bullock TL, Clarkson WD, Kent HM, Stewart M: 1.6 Ȧ structure of nuclear transport factor 2 (NTF2). J Mol Biol 1996, in press. This paper reports a strong structural similarity between NTF2 and an enzyme, raising the possibility of an unanticipated enzymatic activity of the factor.
    • (1996) J Mol Biol
    • Bullock, T.L.1    Clarkson, W.D.2    Kent, H.M.3    Stewart, M.4
  • 20
    • 0028929866 scopus 로고
    • Crystal structure of the nuclear Ras-related protein Ran in its GDP-bound form
    • Scheffzek K, Klebe C, Tritz-Wolf K, Kabsch W, Wittinghofer A: Crystal structure of the nuclear Ras-related protein Ran In its GDP-bound form. Nature 1995, 374:378-380.
    • (1995) Nature , vol.374 , pp. 378-380
    • Scheffzek, K.1    Klebe, C.2    Tritz-Wolf, K.3    Kabsch, W.4    Wittinghofer, A.5
  • 21
    • 0028774336 scopus 로고
    • Crystal structure of scytalone dehydratase - A disease determinant of the rice pathogen, Magnaporthe grisea
    • Lundqvist T, Rice J, Hodge CN, Basarab GS, Pierce J, Lindqvist Y: Crystal structure of scytalone dehydratase - a disease determinant of the rice pathogen, Magnaporthe grisea. Structure 1994, 2:937-944.
    • (1994) Structure , vol.2 , pp. 937-944
    • Lundqvist, T.1    Rice, J.2    Hodge, C.N.3    Basarab, G.S.4    Pierce, J.5    Lindqvist, Y.6
  • 22
    • 0029608909 scopus 로고
    • Ribosomal proteins and elongation factors
    • Liljas A, Garber M: Ribosomal proteins and elongation factors. Curr Opin Struct Biol 1995, 5:721-727.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 721-727
    • Liljas, A.1    Garber, M.2
  • 23
    • 0026687213 scopus 로고
    • The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA
    • Ramakrisnan V, White SW: The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature 1992, 358:768-771.
    • (1992) Nature , vol.358 , pp. 768-771
    • Ramakrisnan, V.1    White, S.W.2
  • 24
    • 0029041105 scopus 로고
    • NMR solution structure of a dsRNa binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5
    • Bycroft M, Grünert S, Murzin AG, Proctor M, St Johnston D: NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5. EMBO J 1995, 14:3563-3571. Staufen protein is required for the localization of maternal mRNAs to op-posite poles of the Drosophila egg. It contains five copies of the double stranded RNA binding motif. This paper reports the solution structure for the third motif.
    • (1995) EMBO J , vol.14 , pp. 3563-3571
    • Bycroft, M.1    Grünert, S.2    Murzin, A.G.3    Proctor, M.4    St Johnston, D.5
  • 26
    • 0029182369 scopus 로고
    • A ribosomal protein module in EF-G and DNA gyrase
    • Murzin AG: A ribosomal protein module in EF-G and DNA gyrase. Nat Struct Biol 1995, 2:25-26.
    • (1995) Nat Struct Biol , vol.2 , pp. 25-26
    • Murzin, A.G.1
  • 28
    • 0030067634 scopus 로고    scopus 로고
    • The crystal structure of the GroES co-chaperonin at 2.8 Ȧ resolution
    • Hunt JF, Weaver AJ, Landry SJ, Gierasch L, Deisenhofer J: The crystal structure of the GroES co-chaperonin at 2.8 Ȧ resolution. Nature 1996, 379:37-45. See annotation [29•].
    • (1996) Nature , vol.379 , pp. 37-45
    • Hunt, J.F.1    Weaver, A.J.2    Landry, S.J.3    Gierasch, L.4    Deisenhofer, J.5
  • 29
    • 0030024540 scopus 로고    scopus 로고
    • Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae
    • Mande SC, Mehra V, Bloom BR, Hol WGJ: Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae. Science 1996, 271:203-207. The structures of GroES and its homologue are the first 'hot' structures to be published this year.
    • (1996) Science , vol.271 , pp. 203-207
    • Mande, S.C.1    Mehra, V.2    Bloom, B.R.3    Hol, W.G.J.4
  • 30
    • 0016345760 scopus 로고
    • Chemical and biological evolution of a nucleotide-binding protein
    • Rossmann MG, Moras D, Olsen KW: Chemical and biological evolution of a nucleotide-binding protein. Nature 1974, 250:194-199.
    • (1974) Nature , vol.250 , pp. 194-199
    • Rossmann, M.G.1    Moras, D.2    Olsen, K.W.3
  • 32
    • 0028977970 scopus 로고
    • Crystal structure of Escherichia coli quinone reductase complexed with NADPH
    • Thorn JM, Barton JD, Dixon NE, Ollis DL, Edwards KJ: Crystal structure of Escherichia coli quinone reductase complexed with NADPH. J Mol Biol 1995, 249:785-799.
    • (1995) J Mol Biol , vol.249 , pp. 785-799
    • Thorn, J.M.1    Barton, J.D.2    Dixon, N.E.3    Ollis, D.L.4    Edwards, K.J.5
  • 34
    • 0028492329 scopus 로고
    • A tale of two proteinases
    • Carrel RW, Lesk AM: A tale of two proteinases. Nat Struct Biol 1994,1:492-494. This news and views article discusses the structural and evolutionary relationship between the chymotrypsin family of serine proteinases and the family of viral 3C cysteine proteinases, the prediction of which has been confirmed recently by the determination of the first two structures for the latter family.
    • (1994) Nat Struct Biol , vol.1 , pp. 492-494
    • Carrel, R.W.1    Lesk, A.M.2
  • 35
    • 0029042511 scopus 로고
    • Crystal structure of the 205 proteasome from the archaeon T. acidophilum at 3.4 Ȧ resolution
    • Löwe J, Stock D, Jap B, Zwickl P, Baumeister W, Huber R: Crystal structure of the 205 proteasome from the archaeon T. acidophilum at 3.4 Ȧ resolution. Science 1995, 268:533-539. Previous electron microscopy studies showed that the chaperonin GroEL, which promotes protein folding, and the proteasome, which catalyzes protein degradation, have strikingly similar oligomeric architectures. After both structures have been solved to atomic resolution, the folds of their subunits appeared very different [27•].
    • (1995) Science , vol.268 , pp. 533-539
    • Löwe, J.1    Stock, D.2    Jap, B.3    Zwickl, P.4    Baumeister, W.5    Huber, R.6
  • 36
    • 0028786346 scopus 로고
    • Three-dimensional structure of human lysosomal aspartylglucosaminidase
    • Oinonen C, Tikkanen R, Rouvinen J, Peltonen L: Three-dimensional structure of human lysosomal aspartylglucosaminidase. Nat Struct Biol 1995, 2:1102-1108. This paper presents the structure of a new member of the Ntn hydrolase family [14••]. This enzyme is directly linked to the inherited disease aspartylglucosaminuria, which is caused by mutation of its gene.
    • (1995) Nat Struct Biol , vol.2 , pp. 1102-1108
    • Oinonen, C.1    Tikkanen, R.2    Rouvinen, J.3    Peltonen, L.4
  • 37
    • 0030021264 scopus 로고    scopus 로고
    • Structure of the multifunctional loops in the nonclassical ATP-binding fold of glutathione synthetase
    • Hibi T, Nishioka T, Kato H, Tanizawa K, Fukui T, Katsube Y, Uda J: Structure of the multifunctional loops in the nonclassical ATP-binding fold of glutathione synthetase. Nat Struct Biol 1996, 3:16-18. This paper presents the structure of glutathione synthetase complexed with an affinity labelling reagent of the ATP-binding site. Although this ATP-binding fold is called non-classical in the title, it soon may turn out to be a major fold.
    • (1996) Nat Struct Biol , vol.3 , pp. 16-18
    • Hibi, T.1    Nishioka, T.2    Kato, H.3    Tanizawa, K.4    Fukui, T.5    Katsube, Y.6    Uda, J.7
  • 38
    • 0028151598 scopus 로고
    • Vancomycin resistance: Structure of D-alanine:D-alanine ligase at 2.3 Ȧ resolution
    • Fan C, Moews PC, Walsh CT, Knox JR: Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 Ȧ resolution. Science 1994, 266:439-443.
    • (1994) Science , vol.266 , pp. 439-443
    • Fan, C.1    Moews, P.C.2    Walsh, C.T.3    Knox, J.R.4
  • 39
    • 0028860295 scopus 로고
    • A common fold for peptide synthetases cleaving ATP to ADP: Glutathione synthetase and D-alanine:D-alanine ligase of Escherichia coli
    • Fan C, Moews PC, Shi Y, Walsh CT, Knox JR: A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:D-alanine ligase of Escherichia coli. Proc Natl Acad Sci USA 1995, 92:1172-1176. A previous report [38] on the D-Ala-D-Ala ligase structure and its similarity to glutathione synthetase is completed here with a detailed structural comparison of the two enzymes and their ATP-binding sites.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 1172-1176
    • Fan, C.1    Moews, P.C.2    Shi, Y.3    Walsh, C.T.4    Knox, J.R.5
  • 40
    • 0028085434 scopus 로고
    • Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase
    • Waldrop GL, Rayment I, Holden HM: Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase. Biochemistry 1994, 33:10249-10256.
    • (1994) Biochemistry , vol.33 , pp. 10249-10256
    • Waldrop, G.L.1    Rayment, I.2    Holden, H.M.3
  • 41
    • 0028276977 scopus 로고
    • The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5 Ȧ resolution
    • Wolodko WT, Fraser ME, James MNG, Bridger WA: The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5 Ȧ resolution. J Biol Cbem 1994, 269:10883-10890.
    • (1994) J Biol Cbem , vol.269 , pp. 10883-10890
    • Wolodko, W.T.1    Fraser, M.E.2    James, M.N.G.3    Bridger, W.A.4
  • 42
    • 0030062938 scopus 로고    scopus 로고
    • Biotin carboxylase comes into the fold
    • Artymiuk PJ, Poirrette AR, Rice DW, Willett P: Biotin carboxylase comes into the fold. Nat Struct Biol 1996, 3:128-132. This paper describes structural and functional similarities between three of the four enzymes known to share the ATP-grasp fold.
    • (1996) Nat Struct Biol , vol.3 , pp. 128-132
    • Artymiuk, P.J.1    Poirrette, A.R.2    Rice, D.W.3    Willett, P.4
  • 43
    • 0029911754 scopus 로고    scopus 로고
    • Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites
    • Herzberg O, Chen CCH, Kapadia G, McGuire M, Carroll L, Noh SJ, Dunaway-Mariano D: Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Proc Natl Acad Sci USA 1996, 93:2652-2657. The crystal structure of pyruvate phosphate dikinase reported here reveals that the enzyme is exquisitely designed to utilize the swiveling-domain mechanism of phosphotransfer from ATP to pyruvate.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 2652-2657
    • Herzberg, O.1    Chen, C.C.H.2    Kapadia, G.3    McGuire, M.4    Carroll, L.5    Noh, S.J.6    Dunaway-Mariano, D.7
  • 44
    • 0029056202 scopus 로고
    • An enzymesubstrate complex involved in bacterial cell wall biosynthesis
    • Benson TE, Filman DJ, Walsh CT, Hogle JM: An enzymesubstrate complex involved in bacterial cell wall biosynthesis. Nat Struct Biol 1995, 2:644-653.
    • (1995) Nat Struct Biol , vol.2 , pp. 644-653
    • Benson, T.E.1    Filman, D.J.2    Walsh, C.T.3    Hogle, J.M.4
  • 45
    • 0026071385 scopus 로고
    • Three-dimensional structure of p-cresol methylhydroxylase (Flavocytochrome c) from Pseudomonas putida at 3.0 Ȧ resolution
    • Mathews FS, Chen Z, Bellamy HD, Mclntire WS: Three-dimensional structure of p-cresol methylhydroxylase (Flavocytochrome c) from Pseudomonas putida at 3.0 Ȧ resolution. Biochemistry 1991, 30:238-247.
    • (1991) Biochemistry , vol.30 , pp. 238-247
    • Mathews, F.S.1    Chen, Z.2    Bellamy, H.D.3    Mclntire, W.S.4
  • 47
    • 0029026444 scopus 로고
    • A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development
    • Mushecian AR, Koonin EV: A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development Protein Sci 1995, 4:1 243-1244.
    • (1995) Protein Sci , vol.4 , pp. 1243-1244
    • Mushecian, A.R.1    Koonin, E.V.2
  • 49
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ: MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991, 24:946-960.
    • (1991) J Appl Crystallogr , vol.24 , pp. 946-960
    • Kraulis, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.