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(-) Description

Title :  CRYSTAL STRUCTURE OF SIALIC ACID SYNTHASE NEUB-INHIBITOR COMPLEX
 
Authors :  F. Liu, H. J. Lee, N. C. J. Strynadka, M. E. Tanner
Date :  25 Aug 09  (Deposition) - 15 Sep 09  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Neub, Inhibitor, Tim Barrel, Sialic Acid Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Liu, H. J. Lee, N. C. J. Strynadka, M. E. Tanner
The Inhibition Of Neisseria Meningitidis Sialic Acid Synthase By A Tetrahedral Intermediate Analog.
Biochemistry V. 48 9194 2009
PubMed-ID: 19719325  |  Reference-DOI: 10.1021/BI9012758

(-) Compounds

Molecule 1 - POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCWORI
    Expression System StrainBL21
    Expression System Taxid511693
    MutationYES
    Organism ScientificNEISSERIA MENINGITIDIS
    Organism Taxid491
    StrainSEROGROUP B
    SynonymSYNC PROTEIN, SIALIC ACID SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric Unit (6, 17)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3LMR1Ligand/Ion(2S)-2-HYDROXYBUTANEDIOIC ACID
4MN1Ligand/IonMANGANESE (II) ION
5MSE9Mod. Amino AcidSELENOMETHIONINE
6WQP1Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXY-2-O-PHOSPHONO-D-ERYTHRO-L-MANNO-NONONIC ACID
Biological Unit 1 (5, 32)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
3LMR2Ligand/Ion(2S)-2-HYDROXYBUTANEDIOIC ACID
4MN-1Ligand/IonMANGANESE (II) ION
5MSE18Mod. Amino AcidSELENOMETHIONINE
6WQP2Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXY-2-O-PHOSPHONO-D-ERYTHRO-L-MANNO-NONONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:25 , LYS A:53 , GLN A:55 , ASN A:74 , MSE A:83 , THR A:110 , PHE A:112 , LYS A:129 , SER A:132 , SER A:154 , ASN A:184 , TYR A:186 , SER A:213 , HIS A:215 , HIS A:236 , PRO A:246 , ASP A:247 , MN A:1351 , HOH A:2141 , HOH A:2310 , HOH A:2311 , HOH A:2312BINDING SITE FOR RESIDUE WQP A1350
2AC2SOFTWAREHIS A:215 , HIS A:236 , WQP A:1350 , HOH A:2312BINDING SITE FOR RESIDUE MN A1351
3AC3SOFTWAREGLN A:2 , MSE A:198 , SER A:202 , LEU A:228 , GLY A:229 , GLY A:230BINDING SITE FOR RESIDUE ACT A1352
4AC4SOFTWARELYS A:35 , THR A:188 , PRO A:189 , THR A:216 , LEU A:217 , HOH A:2313BINDING SITE FOR RESIDUE EDO A1353
5AC5SOFTWARELYS A:275 , THR A:277 , ILE A:278 , LYS A:286 , HOH A:2253 , HOH A:2314BINDING SITE FOR RESIDUE EDO A1354
6AC6SOFTWAREASP A:218 , ASN A:219 , TYR A:220 , HOH A:2227 , HOH A:2315 , HOH A:2316BINDING SITE FOR RESIDUE EDO A1355
7AC7SOFTWAREPRO A:72 , ALA A:75 , ASP A:76 , HOH A:2078BINDING SITE FOR RESIDUE EDO A1356
8AC8SOFTWAREHIS A:265 , HOH A:2317 , HOH A:2318 , HOH A:2320 , HOH A:2321 , HOH A:2322BINDING SITE FOR RESIDUE LMR A1357

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WQP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:186 -Pro A:187
2Arg A:314 -Pro A:315

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WQP)

(-) Sequences/Alignments

Asymmetric 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:348
 aligned with Q7DDU0_NEIMB | Q7DDU0 from UniProtKB/TrEMBL  Length:349

    Alignment length:348
                                    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       301       311       321       331       341        
         Q7DDU0_NEIMB     2 QNNNEFKIGNRSVGYNHEPLIICEIGINHEGSLKTAFEMVDAAYNAGAEVVKHQTHIVEDEMSDEAKQVIPGNADVSIYEIMERCALNEEDEIKLKEYVESKGMIFISTPFSRAAALRLQRMDIPAYKIGSGECNNYPLIKLVASFGKPIILSTGMNSIESIKKSVEIIREAGVPYALLHCTNIYPTPYEDVRLGGMNDLSEAFPDAIIGLSDHTLDNYACLGAVALGGSILERHFTDRMDRPGPDIVCSMNPDTFKELKQGAHALKLARGGKKDTIIAGEKPTKDFAFASVVADKDIKKGELLSGDNLWVKRPGNGDFSVNEYETLFGKVAACNIRKGAQIKKTDIE 349
               SCOP domains d2wqpa1 A:2-281 automated matches                                                                                                                                                                                                                                                       d2wqpa2 A:282-349 automated matches                                  SCOP domains
               CATH domains ----2wqpA01 A:6-276 Aldolase class I                                                                                                                                                                                                                                               ------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------NeuB-2wqpA02 A:40-276                                                                                                                                                                                                                        --------------SAF-2wqpA01 A:291-349                                       Pfam domains
         Sec.struct. author .....ee....ee......eeeee.......hhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eee......hhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeee........hhhhh....hhhhhhhh..........................eeeee..........hhhhh.hhhhhhhhhh.hhhhhhhh..........hhhhhhhhh.eeee..............eeee........hhhhhhhh..............hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wqp A   2 QNNNEFKIGNRSVGYNHEPLIICEIGINHEGSLKTAFEmVDAAYNAGAEVVKHQTHIVEDEmSDEAKQVIPGNADVSIYEImERCALNEEDEIKLKEYVESKGmIFISTLFSRAAALRLQRmDIPAYKIGSGECNNYPLIKLVASFGKPIILSTGmNSIESIKKSVEIIREAGVPYALLHCTNIYPTPYEDVRLGGmNDLSEAFPDAIIGLSDHTLDNYACLGAVALGGSILERHFTDRmDRPGPDIVCSmNPDTFKELKQGAHALKLARGGKKDTIIAGEKPTKDFAFASVVADKDIKKGELLSGDNLWVKRPGNGDFSVNEYETLFGKVAACNIRKGAQIKKTDIE 349
                                    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       301       311       321       331       341        
                                                                 40-MSE                 63-MSE              83-MSE               105-MSE           123-MSE                           157-MSE                                  198-MSE                                    241-MSE    252-MSE                                                                                             

   Legend:   → Mismatch (orange background)
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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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7DDU0_NEIMB | Q7DDU0)
molecular function
    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.
biological process
    GO:0016051    carbohydrate biosynthetic process    The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

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        Q7DDU0_NEIMB | Q7DDU04ipi 4ipj

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