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(-) Description

Title :  STRUCTURE OF THE Y137A MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE, N-ACETYL-D-MANNOSAMINE AND N-ACETYLNEURAMINIC ACID
 
Authors :  I. Campeotto, S. E. V. Phillips, A. R. Pearson, A. Nelson, A. Berry
Date :  03 Jul 13  (Deposition) - 19 Feb 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase, Directed Evolution, Substrate Specificity, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. D. Daniels, I. Campeotto, M. W. Van Der Kamp, A. H. Bolt, C. H. Trinh S. E. V. Phillips, A. R. Pearson, A. Nelson, A. J. Mulholland, A. Berry
The Reaction Mechanism Of N-Acetylneuraminic Acid Lyase Revealed By A Combination Of Crystallography, Qm/Mm Simulation And Mutagenesis.
Acs Chem. Biol. V. 9 1025 2014
PubMed-ID: 24521460  |  Reference-DOI: 10.1021/CB500067Z

(-) Compounds

Molecule 1 - N-ACETYLNEURAMINATE LYASE
    ChainsA, B, D
    EC Number4.1.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKNANA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsSCHIFF BASE BETWEEN LYS165 AND N-ACETYLNEURAMINIC ACID
    SynonymN-ACETYLNEURAMINATE PYRUVATE-LYASE, N-ACETYLNEURAMINIC ACID ALDOLASE, NALASE, SIALATE LYASE, SIALIC ACID ALDOLASE, SIALIC ACID LYASE, N-ACETYLNEURAMINIC ACID LYASE
 
Molecule 2 - N-ACETYLNEURAMINATE LYASE
    ChainsC
    EC Number4.1.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKNANA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsSCHIFF BASE BETWEEN LYS165 AND PYRUVATE
    SynonymN-ACETYLNEURAMINATE PYRUVATE-LYASE, N-ACETYLNEURAMINIC ACID ALDOLASE, NALASE, SIALATE LYASE, SIALIC ACID ALDOLASE, SIALIC ACID LYASE, N-ACETYLNEURAMINIC ACID LYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2KPI1Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
3MN91Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE
4SI33Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXY-D-GLYCERO-D-GALACTO-NON-2-ULOSONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:47 , THR A:48 , ILE A:139 , LYS A:165 , THR A:167 , GLY A:189 , TYR A:190 , ASP A:191 , GLU A:192 , GLY A:207 , SER A:208 , PHE A:252 , HOH A:2003BINDING SITE FOR RESIDUE SI3 A1165
2AC2SOFTWARETYR B:43 , GLY B:46 , SER B:47 , THR B:48 , LYS B:165 , THR B:167 , GLY B:189 , ASP B:191 , GLU B:192 , GLY B:207 , SER B:208 , PHE B:252 , HOH B:2004 , HOH B:2021BINDING SITE FOR RESIDUE SI3 B1165
3AC3SOFTWARETYR D:43 , SER D:47 , THR D:48 , LYS D:165 , THR D:167 , GLY D:189 , TYR D:190 , ASP D:191 , GLU D:192 , ILE D:206 , GLY D:207 , SER D:208 , PHE D:252 , HOH D:2009BINDING SITE FOR RESIDUE SI3 D1165
4AC4SOFTWAREILE C:139 , LEU C:142 , KPI C:165 , THR C:167 , GLY C:189 , ASP C:191 , GLU C:192 , GLY C:207 , SER C:208 , PHE C:252BINDING SITE FOR RESIDUE MN9 C1297
5AC5SOFTWAREASP B:170 , HOH B:2014BINDING SITE FOR RESIDUE 1PE B1297

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BWL)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:272 -Pro A:273
2Lys B:272 -Pro B:273
3Lys C:272 -Pro C:273
4Lys D:272 -Pro D:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BWL)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_1PS00665 Dihydrodipicolinate synthase signature 1.NANA_ECOLI41-58
 
 
 
  4A:41-58
B:41-58
C:41-58
D:41-58
2DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.NANA_ECOLI137-167
 
 
 
  4A:138-167
B:138-167
C:138-167
D:138-167

(-) Exons   (0, 0)

(no "Exon" information available for 4BWL)

(-) 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:299
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:299
                              1                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         
           NANA_ECOLI     - --MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 297
               SCOP domains d4bwla_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.eeee...........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: A:138-167        ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwl A  -1 HHHATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVANIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 297
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
           NANA_ECOLI     2 ATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
               SCOP domains d4bwlb_ B: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: B:138-167        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwl B   2 ATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVANIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:296
                                    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      
           NANA_ECOLI     1 MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
               SCOP domains d4bwlc_ C: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh...eeee.hhhhhh...hhhhhhhhh....eeee.....hhhhhhhhhhhh...eeee....hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: C:138-167        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwl C   1 HATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVANIPALSGVKLTLDQINTLVTLPGVGALkQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
                                    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      
                                                                                                                                                                                              165-KPI                                                                                                                               

Chain D from PDB  Type:PROTEIN  Length:298
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:298
                               1                                                                                                                                                                                                                                                                                                      
                               |     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        
           NANA_ECOLI     - ---MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQE 295
               SCOP domains d4bwld_ D: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.eeeee..........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: D:138-167        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwl D  -2 HHHHATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVANIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQE 295
                                     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        

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BWL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BWL)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NANA_ECOLI | P0A6L4)
molecular function
    GO:0008747    N-acetylneuraminate lyase activity    Catalysis of the reaction: N-acetylneuraminate = N-acetyl-D-mannosamine + pyruvate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0019262    N-acetylneuraminate catabolic process    The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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UniProtKB/Swiss-Prot
        NANA_ECOLI | P0A6L41fdy 1fdz 1hl2 1nal 2wkj 2wnn 2wnq 2wnz 2wo5 2wpb 2xfw 2ygy 3lbc 3lbm 3lcf 3lcg 3lch 3lci 3lcl 3lcw 3lcx 4uui

(-) Related Entries Specified in the PDB File

4bwk STRUCTURE OF THE Y137A MUTANT OF E. COLI N- ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE, N -ACETYL-D-MANNOSAMINE AND N-ACETYLNEURAMINIC ACID