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PDBsum entry 1kit

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protein metals links
Hydrolase PDB id
1kit
Jmol
Contents
Protein chain
757 a.a. *
Metals
_CA ×2
Waters ×699
* Residue conservation analysis
PDB id:
1kit
Name: Hydrolase
Title: Vibrio cholerae neuraminidase
Structure: Sialidase. Chain: a. Synonym: neuraminidase. Engineered: yes
Source: Vibrio cholerae. Organism_taxid: 666. Strain: classical ogawa 395. Gene: nanh. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.170    
Authors: G.L.Taylor,S.J.Crennell,E.F.Garman,E.R.Vimr,W.G.Laver
Key ref:
S.Crennell et al. (1994). Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain. Structure, 2, 535-544. PubMed id: 7922030 DOI: 10.1016/S0969-2126(00)00053-8
Date:
21-Jun-96     Release date:   05-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C6E9  (NANH_VIBCH) -  Sialidase
Seq:
Struc:
 
Seq:
Struc:
781 a.a.
757 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.18  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     exo-alpha-(2->3)-sialidase activity     7 terms  

 

 
DOI no: 10.1016/S0969-2126(00)00053-8 Structure 2:535-544 (1994)
PubMed id: 7922030  
 
 
Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain.
S.Crennell, E.Garman, G.Laver, E.Vimr, G.Taylor.
 
  ABSTRACT  
 
BACKGROUND: Vibrio cholerae neuraminidase is part of a mucinase complex which may function in pathogenesis by degrading the mucin layer of the gastrointestinal tract. The neuraminidase, which has been the target of extensive inhibitor studies, plays a subtle role in the pathology of the bacterium, by processing higher order gangliosides to GM1, the receptor for cholera toxin. RESULTS: We report here the X-ray crystal structure of V. cholerae neuraminidase at 2.3 A resolution. The 83 kDa enzyme folds into three distinct domains. The central catalytic domain has the canonical neuraminidase beta-propeller fold, and is flanked by two domains which possess identical legume lectin-like topologies but without the usual metal-binding loops. The active site has many features in common with other viral and bacterial neuraminidases but, uniquely, has an essential Ca2+ ion which plays a crucial structural role. CONCLUSIONS: The environment of the small intestine requires V. cholerae to secrete several adhesins, and it is known that its neuraminidase can bind to cell surfaces, and remain active. The unexpected lectin-like domains possibly mediate this attachment. These bacterial lectin folds represent additional members of a growing lectin superfamily.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a), (b) MOLSCRIPT [44] drawings of orthogonal views of the two wings, viewed after superposition of wing-2 onto wing-1 as detailed in Table 1. Figure 3. (a), (b) MOLSCRIPT [[4]44] drawings of orthogonal views of the two wings, viewed after superposition of wing-2 onto wing-1 as detailed in [5]Table 1.
Figure 6.
Figure 6. MOLSCRIPT and Raster 3D (E Merritt unpublished program) drawings of the active sites of (a) cholera NA, showing residues within 5 å of DANA, and the position of the Ca^2+ ion essential for activity, (b) salmonella NA showing residues which interact with DANA [14], and (c) influenza NA from virus A/tern/Australia/G70C/75 NA, an N9 subtype, showing residues which interact with DANA [26]. Figure 6. MOLSCRIPT and Raster 3D (E Merritt unpublished program) drawings of the active sites of (a) cholera NA, showing residues within 5 å of DANA, and the position of the Ca^2+ ion essential for activity, (b) salmonella NA showing residues which interact with DANA [[5]14], and (c) influenza NA from virus A/tern/Australia/G70C/75 NA, an N9 subtype, showing residues which interact with DANA [[6]26].
 
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 535-544) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21305698 H.Hinou, R.Miyoshi, Y.Takasu, H.Kai, M.Kurogochi, S.Arioka, X.D.Gao, N.Miura, N.Fujitani, S.Omoto, T.Yoshinaga, T.Fujiwara, T.Noshi, H.Togame, H.Takemoto, and S.Nishimura (2011).
A strategy for neuraminidase inhibitors using mechanism-based labeling information.
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21240549 T.Lieke, D.Gröbe, V.Blanchard, D.Grunow, R.Tauber, M.Zimmermann-Kordmann, T.Jacobs, and W.Reutter (2011).
Invasion of Trypanosoma cruzi into host cells is impaired by N-propionylmannosamine and other N-acylmannosamines.
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19023603 D.C.Soares, P.N.Barlow, D.J.Porteous, and R.S.Devon (2009).
An interrupted beta-propeller and protein disorder: structural bioinformatics insights into the N-terminus of alsin.
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19564377 D.Parker, G.Soong, P.Planet, J.Brower, A.J.Ratner, and A.Prince (2009).
The NanA neuraminidase of Streptococcus pneumoniae is involved in biofilm formation.
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19594936 E.M.Quistgaard, and S.S.Thirup (2009).
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families.
  BMC Struct Biol, 9, 46.  
19124471 H.Connaris, P.R.Crocker, and G.L.Taylor (2009).
Enhancing the Receptor Affinity of the Sialic Acid-binding Domain of Vibrio cholerae Sialidase through Multivalency.
  J Biol Chem, 284, 7339-7351.
PDB code: 2w68
19191477 N.Koropatkin, E.C.Martens, J.I.Gordon, and T.J.Smith (2009).
Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.
  Biochemistry, 48, 1532-1542.
PDB codes: 3ehm 3ehn
19687228 S.Uchiyama, A.F.Carlin, A.Khosravi, S.Weiman, A.Banerjee, D.Quach, G.Hightower, T.J.Mitchell, K.S.Doran, and V.Nizet (2009).
The surface-anchored NanA protein promotes pneumococcal brain endothelial cell invasion.
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18784084 M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, and N.C.Strynadka (2008).
The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN.
  J Biol Chem, 283, 31279-31283.
PDB code: 3ecq
18218621 S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, and G.L.Taylor (2008).
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.
  J Biol Chem, 283, 9080-9088.
PDB codes: 2bf6 2vk5 2vk6 2vk7
17449623 C.Geslin, M.Gaillard, D.Flament, K.Rouault, M.Le Romancer, D.Prieur, and G.Erauso (2007).
Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi.
  J Bacteriol, 189, 4510-4519.  
16575518 E.Villar, and I.M.Barroso (2006).
Role of sialic acid-containing molecules in paramyxovirus entry into the host cell: a minireview.
  Glycoconj J, 23, 5.  
16352831 S.E.Haydel, and J.E.Clark-Curtiss (2006).
The Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller.
  J Bacteriol, 188, 150-159.  
15864320 J.N.Watson, T.L.Knoll, J.H.Chen, D.T.Chou, T.J.Borgford, and A.J.Bennet (2005).
Use of conformationally restricted pyridinium alpha-D-N-acetylneuraminides to probe specificity in bacterial and viral sialidases.
  Biochem Cell Biol, 83, 115-122.  
15608653 K.Stummeyer, A.Dickmanns, M.Mühlenhoff, R.Gerardy-Schahn, and R.Ficner (2005).
Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.
  Nat Struct Mol Biol, 12, 90-96.
PDB codes: 1v0e 1v0f
16239725 S.L.Newstead, J.N.Watson, A.J.Bennet, and G.Taylor (2005).
Galactose recognition by the carbohydrate-binding module of a bacterial sialidase.
  Acta Crystallogr D Biol Crystallogr, 61, 1483-1491.
PDB codes: 2bq9 2bzd
16323045 S.Smith, M.Hyde, and M.R.Pincus (2005).
Comparison of the predicted structures of loops in the ras-SOS protein bound to a single ras-p21 protein with the crystallographically determined structures in SOS bound to two ras-p21 proteins.
  Protein J, 24, 391-398.  
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
14613940 C.Tringali, N.Papini, P.Fusi, G.Croci, G.Borsani, A.Preti, P.Tortora, G.Tettamanti, B.Venerando, and E.Monti (2004).
Properties of recombinant human cytosolic sialidase HsNEU2. The enzyme hydrolyzes monomerically dispersed GM1 ganglioside molecules.
  J Biol Chem, 279, 3169-3179.  
15007099 E.R.Vimr, K.A.Kalivoda, E.L.Deszo, and S.M.Steenbergen (2004).
Diversity of microbial sialic acid metabolism.
  Microbiol Mol Biol Rev, 68, 132-153.  
14973124 F.Alberto, C.Bignon, G.Sulzenbacher, B.Henrissat, and M.Czjzek (2004).
The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.
  J Biol Chem, 279, 18903-18910.
PDB codes: 1utw 1uyp
15226294 I.Moustafa, H.Connaris, M.Taylor, V.Zaitsev, J.C.Wilson, M.J.Kiefel, M.von Itzstein, and G.Taylor (2004).
Sialic acid recognition by Vibrio cholerae neuraminidase.
  J Biol Chem, 279, 40819-40826.
PDB codes: 1w0o 1w0p
15130470 M.F.Amaya, A.G.Watts, I.Damager, A.Wehenkel, T.Nguyen, A.Buschiazzo, G.Paris, A.C.Frasch, S.G.Withers, and P.M.Alzari (2004).
Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.
  Structure, 12, 775-784.
PDB codes: 1s0i 1s0j 1s0k 2ah2
15502328 S.Newstead, C.H.Chien, M.Taylor, and G.Taylor (2004).
Crystallization and atomic resolution X-ray diffraction of the catalytic domain of the large sialidase, nanI, from Clostridium perfringens.
  Acta Crystallogr D Biol Crystallogr, 60, 2063-2066.  
15211517 T.Haselhorst, J.C.Wilson, R.J.Thomson, S.McAtamney, J.G.Menting, R.L.Coppel, and M.von Itzstein (2004).
Saturation transfer difference (STD) 1H-NMR experiments and in silico docking experiments to probe the binding of N-acetylneuraminic acid and derivatives to Vibrio cholerae sialidase.
  Proteins, 56, 346-353.  
12657781 A.J.Oakley, T.Heinrich, C.A.Thompson, and M.C.Wilce (2003).
Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching.
  Acta Crystallogr D Biol Crystallogr, 59, 627-636.
PDB code: 1igo
14573944 E.Garman, and J.W.Murray (2003).
Heavy-atom derivatization.
  Acta Crystallogr D Biol Crystallogr, 59, 1903-1913.  
14517945 V.Seyrantepe, H.Poupetova, R.Froissart, M.T.Zabot, I.Maire, and A.V.Pshezhetsky (2003).
Molecular pathology of NEU1 gene in sialidosis.
  Hum Mutat, 22, 343-352.  
12419220 A.Buschiazzo, M.F.Amaya, M.L.Cremona, A.C.Frasch, and P.M.Alzari (2002).
The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis.
  Mol Cell, 10, 757-768.
PDB codes: 1mr5 1ms0 1ms1 1ms3 1ms4 1ms5 1ms8 1ms9
12237289 A.R.Todeschini, M.F.Girard, J.M.Wieruszeski, M.P.Nunes, G.A.DosReis, L.Mendonca-Previato, and J.O.Previato (2002).
trans-Sialidase from Trypanosoma cruzi binds host T-lymphocytes in a lectin manner.
  J Biol Chem, 277, 45962-45968.  
11994155 D.R.Leggate, J.M.Bryant, M.B.Redpath, D.Head, P.W.Taylor, and J.P.Luzio (2002).
Expression, mutagenesis and kinetic analysis of recombinant K1E endosialidase to define the site of proteolytic processing and requirements for catalysis.
  Mol Microbiol, 44, 749-760.  
12071958 G.Montagna, M.L.Cremona, G.Paris, M.F.Amaya, A.Buschiazzo, P.M.Alzari, and A.C.Frasch (2002).
The trans-sialidase from the african trypanosome Trypanosoma brucei.
  Eur J Biochem, 269, 2941-2950.  
11799177 H.Connaris, T.Takimoto, R.Russell, S.Crennell, I.Moustafa, A.Portner, and G.Taylor (2002).
Probing the sialic acid binding site of the hemagglutinin-neuraminidase of Newcastle disease virus: identification of key amino acids involved in cell binding, catalysis, and fusion.
  J Virol, 76, 1816-1824.  
11880627 J.S.Richardson, and D.C.Richardson (2002).
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.
  Proc Natl Acad Sci U S A, 99, 2754-2759.  
11308029 R.G.Kleineidam, S.Kruse, P.Roggentin, and R.Schauer (2001).
Elucidation of the role of functional amino acid residues of the small sialidase from Clostridium perfringens by site-directed mutagenesis.
  Biol Chem, 382, 313-319.  
10619840 A.Buschiazzo, G.A.Tavares, O.Campetella, S.Spinelli, M.L.Cremona, G.París, M.F.Amaya, A.C.Frasch, and P.M.Alzari (2000).
Structural basis of sialyltransferase activity in trypanosomal sialidases.
  EMBO J, 19, 16-24.
PDB codes: 1mz5 1mz6
11092845 S.Mizan, A.Henk, A.Stallings, M.Maier, and M.D.Lee (2000).
Cloning and characterization of sialidases with 2-6' and 2-3' sialyl lactose specificity from Pasteurella multocida.
  J Bacteriol, 182, 6874-6883.  
10647175 E.Garman (1999).
Leaving no element of doubt: analysis of proteins using microPIXE.
  Structure, 7, R291-R299.  
10520997 G.Rudenko, T.Nguyen, Y.Chelliah, T.C.Südhof, and J.Deisenhofer (1999).
The structure of the ligand-binding domain of neurexin Ibeta: regulation of LNS domain function by alternative splicing.
  Cell, 99, 93.
PDB code: 1c4r
10090286 M.M.Prabu, K.Suguna, and M.Vijayan (1999).
Variability in quaternary association of proteins with the same tertiary fold: a case study and rationalization involving legume lectins.
  Proteins, 35, 58-69.  
10450982 P.Florio, R.J.Thomson, A.Alafaci, S.Abo, and M.von Itzstein (1999).
Synthesis of delta4-beta-D-glucopyranosiduronic acids as mimetics of 2,3-unsaturated sialic acids for sialidase inhibition.
  Bioorg Med Chem Lett, 9, 2065-2068.  
9562562 Y.Luo, S.C.Li, M.Y.Chou, Y.T.Li, and M.Luo (1998).
The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity.
  Structure, 6, 521-530.
PDB codes: 1sli 1sll
9020182 C.M.Milner, S.V.Smith, M.B.Carrillo, G.L.Taylor, M.Hollinshead, and R.D.Campbell (1997).
Identification of a sialidase encoded in the human major histocompatibility complex.
  J Biol Chem, 272, 4549-4558.  
9345620 C.S.Wright (1997).
New folds of plant lectins.
  Curr Opin Struct Biol, 7, 631-636.  
  9223510 J.P.Langedijk, F.J.Daus, and J.T.van Oirschot (1997).
Sequence and structure alignment of Paramyxoviridae attachment proteins and discovery of enzymatic activity for a morbillivirus hemagglutinin.
  J Virol, 71, 6155-6167.  
9365983 V.C.Epa (1997).
Modeling the paramyxovirus hemagglutinin-neuraminidase protein.
  Proteins, 29, 264-281.  
9204286 Y.Lindqvist, and G.Schneider (1997).
Circular permutations of natural protein sequences: structural evidence.
  Curr Opin Struct Biol, 7, 422-427.  
8994884 G.Taylor (1996).
Sialidases: structures, biological significance and therapeutic potential.
  Curr Opin Struct Biol, 6, 830-837.  
8913694 M.von Itzstein, and P.Colman (1996).
Design and synthesis of carbohydrate-based inhibitors of protein-carbohydrate interactions.
  Curr Opin Struct Biol, 6, 703-709.  
8591030 A.Gaskell, S.Crennell, and G.Taylor (1995).
The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
  Structure, 3, 1197-1205.
PDB codes: 1eur 1eus 1eut 1euu
8747464 D.D.Leonidas, B.L.Elbert, Z.Zhou, H.Leffler, S.J.Ackerman, and K.R.Acharya (1995).
Crystal structure of human Charcot-Leyden crystal protein, an eosinophil lysophospholipase, identifies it as a new member of the carbohydrate-binding family of galectins.
  Structure, 3, 1379-1393.
PDB code: 1lcl
  7549872 J.N.Varghese, V.C.Epa, and P.M.Colman (1995).
Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase.
  Protein Sci, 4, 1081-1087.
PDB codes: 1nnc 7nn9
7588726 M.Hahn, T.Keitel, and U.Heinemann (1995).
Crystal and molecular structure at 0.16-nm resolution of the hybrid Bacillus endo-1,3-1,4-beta-D-glucan 4-glucanohydrolase H(A16-M).
  Eur J Biochem, 232, 849-858.
PDB code: 2ayh
7981969 E.R.Vimr (1994).
Microbial sialidases: does bigger always mean better?
  Trends Microbiol, 2, 271-277.  
7881905 G.E.Norris, T.J.Stillman, B.F.Anderson, and E.N.Baker (1994).
The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.
  Structure, 2, 1049-1059.
PDB code: 1pgs
  7849585 P.M.Colman (1994).
Influenza virus neuraminidase: structure, antibodies, and inhibitors.
  Protein Sci, 3, 1687-1696.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.