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(-) Description

Title :  TRYPANOSOMA RANGELI SIALIDASE IN COMPLEX WITH DANA AT 1.6 A
 
Authors :  M. F. Amaya, A. Buschiazzo, T. Nguyen, P. M. Alzari
Date :  20 Oct 02  (Deposition) - 07 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Propeller, Lectin-Like Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Amaya, A. Buschiazzo, T. Nguyen, P. M. Alzari
The High Resolution Structures Of Free And Inhibitor-Bound Trypanosoma Rangeli Sialidase And Its Comparison With T. Cruzi Trans-Sialidase
J. Mol. Biol. V. 325 773 2003
PubMed-ID: 12507479  |  Reference-DOI: 10.1016/S0022-2836(02)01306-2
(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 Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PTRCHIS A
    Fragment: RESIDUE 23-660
    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
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:472 , ARG A:594 , SER A:595 , LYS A:596 , HOH A:1223BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREARG A:227 , LYS A:229 , PHE A:230BINDING SITE FOR RESIDUE SO4 A 802
3AC3SOFTWAREARG A:39 , ARG A:57 , ASP A:63 , MET A:99 , ASP A:100 , TRP A:124 , ARG A:249 , GLN A:287 , ARG A:318 , TYR A:346 , HOH A:819 , HOH A:836 , HOH A:868 , HOH A:882 , HOH A:916 , HOH A:1011 , HOH A:1141 , HOH A:1228BINDING SITE FOR RESIDUE DAN A 700

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:400 -A:414

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N1T)

(-) Exons   (0, 0)

(no "Exon" information available for 1N1T)

(-) 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:628
 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 d1n1ta2 A:1-406 Trypanosoma sialidase                                                                                                                                                                                                                                                                                                                                                                                 ------d1n1ta1 A:413-634 Trypanosoma sialidase, C-terminal domain                                                                                                                                                                     SCOP domains
               CATH domains 1n1tA01 A:1-386  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                              ------------------------------1n1tA02 A:417-618  [code=2.60.120.200, no name defined]                                                                                                                                                   ---------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Laminin_G_3-1n1tA01 A:455-622                                                                                                                                           ------------ 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........eeeeeeeee..eeeeeeee......eeee.......ee.......................eeeeee..eeeeeeeee...........eeeeee....eeeeee..........eeeeee..eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh........------..........eeeeeeeee...eeee......eeee.eeee..eeee.....eeeee.hhhh....hhhhh.eeeeeeeeee......eeeeeeeee......eeeeeeee....eeeee...............eeeeeeeee..eeeeee..ee.....ee.........eeeeeee............eeeeeeeee....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n1t A   1 AASLAPGSSRVELFKRKNSTVPFEESNGTIRERVVHSFRIPTIVNVDGVMVAIADARYETSFDNSFIETAVKYSVDDGATWNTQIAIKNSRASSVSRVMDATVIVKGNKLYILVGSFNKTRNSWTQHRDGSDWEPLLVVGEVTKSAANGKTTATISWGKPVSLKPLFPAEFDGILTKEFVGGVGAAIVASNGNLVYPVQIADMGGRVFTKIMYSEDDGNTWKFAEGRSKFGCSEPAVLEWEGKLIINNRVDGNRRLVYESSDMGKTWVEALGTLSHVWTNSPTSNQQDCQSSFVAVTIEGKRVMLFTHPLNLKGRWMRDRLHLWMTDNQRIFDVGQISIGDENSGYSSVLYKDDKLYSLHEINTNDVYSLVFVRLIGELQLMKSVVRTWKEEDNHLASICTPVVPA------GCGAAVPTAGLVGFLSHSANGSVWEDVYRCVDANVANAERVPNGLKFNGVGGGAVWPVARQGQTRRYQFANYRFTLVATVTIDELPKGTSPLLGAGLEGPGDAKLLGLSYDKNRQWRPLYGAAPASPTGSWELHKKYHVVLTMADRQGSVYVDGQPLAGSGNTVVRGATLPDISHFYIGGPRSKGAPTDSRVTVTNVVLYNRRLNSSEIRTLFLSQDMIGTD 634
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400     |   -  |    420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630    
                                                                                                                                                                                                                                                                                                                                                                                                                                               406    413
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) 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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  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 1n1v 1n1y 1wcs 2a75 2ags 2fhr

(-) Related Entries Specified in the PDB File

1mz5 NATURAL (GLYCOSYLATED) SIALIDASE FROM TRYPANOSOMA RANGELI IN COMPLEX WITH THE INHIBITOR DANA
1mz6 NATURAL (GLYCOSYLATED) SIALIDASE FROM TRYPANOSOMA RANGELI
1n1s TRYPANOSOMA RANGELI SIALIDASE
1n1v TRYPANOSOMA RANGELI SIALIDASE IN COMPLEX WITH DANA
1n1y TRYPANOSOMA RANGELI SIALIDASE IN COMPLEX WITH SIALIC ACID