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(-) Description

Title :  TRYPANOSOMA RANGELI SIALIDASE IN COMPLEX WITH 2,3-DIFLUOROSIALIC ACID (COVALENT INTERMEDIATE)
 
Authors :  M. F. Amaya, P. M. Alzari, A. Buschiazzo
Date :  04 Jul 05  (Deposition) - 22 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Propeller, Covalent Enzyme-Intermediate Complex, Beta- Sandwich, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Watts, P. Oppezzo, S. G. Withers, P. M. Alzari, A. Buschiazzo
Structural And Kinetic Analysis Of Two Covalent Sialosyl-Enzyme Intermediates On Trypanosoma Rangeli Sialidase.
J. Biol. Chem. V. 281 4149 2006
PubMed-ID: 16298994  |  Reference-DOI: 10.1074/JBC.M510677200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIALIDASE
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHISA
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: TRYPANOSOMA RANGELI
    Organism Taxid: 5698

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FSI1Ligand/Ion5-(ACETYLAMINO)-2,6-ANHYDRO-3,5-DIDEOXY-3-FLUORONONONIC ACID
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:469 , ARG A:591 , SER A:592 , LYS A:593 , HOH A:2388BINDING SITE FOR RESIDUE SO4 A 1801
2AC2SOFTWAREARG A:224 , LYS A:226 , PHE A:227 , HOH A:2216BINDING SITE FOR RESIDUE SO4 A 1802
3AC3SOFTWAREARG A:36 , ILE A:37 , ARG A:54 , ASP A:60 , ASP A:97 , TRP A:121 , GLU A:231 , ARG A:246 , ARG A:315 , TYR A:343 , HOH A:1846 , HOH A:1850 , HOH A:1885 , HOH A:2014 , HOH A:2023 , HOH A:2179 , HOH A:2293BINDING SITE FOR RESIDUE FSI A 700

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:397 -A:411

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A75)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A75)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A75)

(-) Exons   (0, 0)

(no "Exon" information available for 2A75)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:632
 aligned with O44049_TRYRA | O44049 from UniProtKB/TrEMBL  Length:660

    Alignment length:634
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649    
         O44049_TRYRA    20 ASALAPGSSRVELFKRKNSTVPFEESNGTIRERVVHSFRIPTIVNVDGVMVATADARYETSFDNSFIETAVKYSVDDGATWNTQIAIKNSRASSVSRVMDATVIVKGNKLYILVGSFNKTRNSWTQHRDGSDWEPLLVVGEVTKSAANGKTTATISWGKPVSLKPLFPAEFDGILTKEFIGGVGAAIVGSNGNLVYPVQIADMGGRVFTKIMYSEDDGNTWKFAEGRSKFGCSEPAVLEWEGKLIINNRVDGNRRLVYESSDMGKTWVEALGTLSHVWTNSPTSNQQDCQSSFVAVTIEGKRVMLFTHPLNLKGRWMRDRLHLWMTDNQRIFDVGQISIGDENSGYSSVLYKDDKLYSLHEINTNDVYSLVFVRFIGELQLMKSVVRTWKEEDNHLASICTPVVPATPPSKGGCGAAVPTAGLVGFLSHSANGSVWEDVYRCVDANVANAERVPNGLKFNGVGGGAVWPVARQGQTRRYQFANYRFTLVATVTIDELPKGTSPLLGAGLEGPGDAKLLGLSYDKNRQWRPLYGAAPASPTGSWELHKKYHVVLTMADRQGSVYVDGQPLAGSGNTVVRGATLPDISHFYIGGPRSKGAPTDSRVTVTNIVLYNRRLNSSEIRTLFLSQDMIGTD 653
               SCOP domains d2a75a2 A:-2-403 automated matches                                                                                                                                                                                                                                                                                                                                                                                    d2  a75a1 A:404-631 automated matches                                                                                                                                                                                                SCOP domains
               CATH domains 2a75A01 A:-2-383  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                             ------------------------------2a75A02 A:414-615  [code=2.60.120.200, no name defined]                                                                                                                                                   ---------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.....eeeee.....eeeee..eeeeeeeeee..eeeeeeeee.........eeeeeeee.......eeeeee.........eeeeeeeeee..eeeeeeeee.....hhhhh.....eeeeeeeeeeeeeee..eeeeeeee...ee.hhhh..ee..eeeeeeee..ee.ee.....eeeeeeeee....eeeeeeee.......ee.........eeeeeeee..eeeeeee.......eeee.......ee.......................eeeeee..eeeeeeeee...........eeeeee....eeeeee..........eeeeee..eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh..........--............eeeeeeeee...eeee......eeee.eeee..eeee.....eeeee.hhhh....hhhhhh.eeeeeeeee......eeeeeeeee......eeeeeeee....eeeee...............eeeeeeeee..eeeeee..ee.....ee.........eeeeeee............eeeeeeeee....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a75 A  -2 MASLAPGSSRVELFKRKNSTVPFEESNGTIRERVVHSFRIPTIVNVDGVMVAIADARYETSFDNSFIETAVKYSVDDGATWNTQIAIKNSRASSVSRVMDATVIVKGNKLYILVGSFNKTRNSWTQHRDGSDWEPLLVVGEVTKSAANGKTTATISWGKPVSLKPLFPAEFDGILTKEFIGGVGAAIVASNGNLVYPVQIADMGGRVFTKIMYSEDDGNTWKFAEGRSKFGCSEPAVLEWEGKLIINNRVDGNRRLVYESSDMGKTWVEALGTLSHVWTNSPTSNQQDCQSSFVAVTIEGKRVMLFTHPLNLKGRWMRDRLHLWMTDNQRIFDVGQISIGDENSGYSSVLYKDDKLYSLHEINTNDVYSLVFVRLIGELQLMKSVVRTWKEEDNHLASICTPVVPATP--KGGCGAAVPTAGLVGFLSHSANGSVWEDVYRCVDANVANAERVPNGLKFNGVGGGAVWPVARQGQTRRYQFANYRFTLVATVTIDELPKGTSPLLGAGLEGPGDAKLLGLSYDKNRQWRPLYGAAPASPTGSWELHKKYHVVLTMADRQGSVYVDGQPLAGSGNTVVRGATLPDISHFYIGGPRSKGAPTDSRVTVTNVVLYNRRLNSSEIRTLFLSQDMIGTD 631
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       | -|      417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627    
                                                                                                                                                                                                                                                                                                                                                                                                                                                 405  |                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                    408
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A75)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O44049_TRYRA | O44049)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the 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.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.

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  2a75
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  3.2.1.18
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        O44049_TRYRA | O44049: 1mz5 1mz6 1n1s 1n1t 1n1v 1n1y 1wcs 2ags 2fhr

(-) Related Entries Specified in the PDB File

1n1s CRYSTAL STRUCTURE OF TRYPANOSOMA RANGELI SIALIDASE
2ags CRYSTAL STRUCTURE OF TRYPANOSOMA RANGELI SIALIDASE IN INCOMPLEX WITH 2-KETO-3-DEOXY-D-GLYCERO-D-GALACTO-2,3_ DIFLUORO-NONONIC ACID (2,3-DIFLUORO-KDN)
2ah2 CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI TRANS-SIALIDASE IN COMPLEX WITH 2,3-DIFLUOROSIALIC ACID (COVALENT INTERMEDIATE)