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(-) Description

Title :  STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CMP.
 
Authors :  L. Y. C. Lin, B. Rakic, C. P. C. Chiu, E. Lameignere, W. W. Wakarchuk, S. G. N. C. J. Strynadka
Date :  25 May 11  (Deposition) - 31 Aug 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Y. C. Lin, B. Rakic, C. P. C. Chiu, E. Lameignere, W. W. Wakarchuk, S. G. Withers, N. C. J. Strynadka
Structure And Mechanism Of The Lipooligosaccharide Sialyltransferase From Neisseria Meningitidis
J. Biol. Chem. V. 286 37237 2011
PubMed-ID: 21880735  |  Reference-DOI: 10.1074/JBC.M111.249920

(-) Compounds

Molecule 1 - CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3- SIALYLTRANSFERASE
    Chains: A
    EC Number: 2.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-41B
    Expression System Vector Type: PLASMID
    Fragment: DELTA29NST, RESIDUES 49-370
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP B
    Organism Taxid: 491
    Strain: 126E / NRCC4010
    Synonym: ALPHA 2,3-ST, BETA-GALACTOSIDE ALPHA-2,3-SIALYL TRANSFERASE, LIPOOLIGOSACCHARIDE SIALYLTRANSFERASE, LOS-SPECIFIC SIALYLTRANSFERASE
    Variant: L1 IMMUNOTYPE

 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, 19)

Asymmetric Unit (6, 19)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2C1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MSE11Mod. Amino AcidSELENOMETHIONINE
5PO41Ligand/IonPHOSPHATE ION
6SO43Ligand/IonSULFATE ION
Biological Unit 1 (5, 36)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2C-1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
3EDO4Ligand/Ion1,2-ETHANEDIOL
4MSE22Mod. Amino AcidSELENOMETHIONINE
5PO42Ligand/IonPHOSPHATE ION
6SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:59 , LEU A:254 , GLY A:255 , ALA A:278 , HIS A:280 , PRO A:281 , VAL A:298 , ILE A:299 , GLU A:300 , SER A:322 , GLY A:323 , ALA A:324 , PO4 A:1376 , HOH A:2083 , HOH A:2174 , HOH A:2198 , HOH A:2216 , HOH A:2217BINDING SITE FOR RESIDUE C A 1375
2AC2SOFTWAREASN A:117 , PHE A:118 , HIS A:280 , ARG A:282 , C A:1375 , HOH A:2006 , HOH A:2217 , HOH A:2218 , HOH A:2219BINDING SITE FOR RESIDUE PO4 A 1376
3AC3SOFTWAREASN A:113 , SER A:115 , LEU A:143 , GLU A:144 , VAL A:146 , SER A:147 , ALA A:150 , THR A:154 , HOH A:2047BINDING SITE FOR RESIDUE 1PE A 1377
4AC4SOFTWAREASN A:86 , GLU A:87 , LYS A:203 , ARG A:226BINDING SITE FOR RESIDUE SO4 A 1378
5AC5SOFTWAREHIS A:71 , GLU A:74 , ARG A:137 , ARG A:251 , ASN A:273 , HOH A:2220BINDING SITE FOR RESIDUE SO4 A 1379
6AC6SOFTWAREGLY A:178 , ASP A:179 , GLU A:180 , SER A:288BINDING SITE FOR RESIDUE SO4 A 1380
7AC7SOFTWARELEU A:59 , VAL A:63 , ASP A:164 , GLY A:166 , HOH A:2005 , HOH A:2084BINDING SITE FOR RESIDUE EDO A 1381
8AC8SOFTWARELYS A:88 , PRO A:279 , LEU A:293 , TYR A:297 , VAL A:298 , ILE A:299 , TYR A:302 , HOH A:2174BINDING SITE FOR RESIDUE EDO A 1382

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YK5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LST_NEIMB_004 *N94KLST_NEIMB  ---  ---AN94K
2UniProtVAR_LST_NEIMB_005 *R102WLST_NEIMB  ---  ---AW102W
3UniProtVAR_LST_NEIMB_006 *S129ALST_NEIMB  ---  ---AA129A
4UniProtVAR_LST_NEIMB_007 *G168ILST_NEIMB  ---  ---AI168I
5UniProtVAR_LST_NEIMB_008 *T242ALST_NEIMB  ---  ---AA242A
6UniProtVAR_LST_NEIMB_009 *K273NLST_NEIMB  ---  ---AN273N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LST_NEIMB_004 *N94KLST_NEIMB  ---  ---AN94K
2UniProtVAR_LST_NEIMB_005 *R102WLST_NEIMB  ---  ---AW102W
3UniProtVAR_LST_NEIMB_006 *S129ALST_NEIMB  ---  ---AA129A
4UniProtVAR_LST_NEIMB_007 *G168ILST_NEIMB  ---  ---AI168I
5UniProtVAR_LST_NEIMB_008 *T242ALST_NEIMB  ---  ---AA242A
6UniProtVAR_LST_NEIMB_009 *K273NLST_NEIMB  ---  ---AN273N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YK5)

(-) Exons   (0, 0)

(no "Exon" information available for 2YK5)

(-) 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:326
 aligned with LST_NEIMB | P72097 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:326
                                                                                                                                                                                                                                                                                                                                                            371   
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  |   
            LST_NEIMB    49 PVNLIFCYTILQMKVAERIMAQHPGERFYVVLMSENRNEKYDYYFNQIKDKAERAYFFHLPYGLNKSFNFIPTMAELKVKSMLLPKVKRIYLASLEKVSIAAFLSTYPDAEIKTFDDGTGNLIQSSSYLGDEFSVNGTIKRNFARMMIGDWSIAKTRNASDEHYTIFKGLKNIMDDGRRKMTYLPLFDASELKTGDETGGTVRILLGSPDKEMKEISEKAAKNFKIQYVAPHPRQTYGLSGVTTLNSPYVIEDYILREIKKNPHTRYEIYTFFSGAALTMKDFPNVHVYALKPASLPEDYWLKPVYALFTQSGIPILTFDDKN---   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhh.eeeeee.............hhhhhhhhhh......eeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeee..............eeee.................eeeeee...hhhhhhhhhhhhhhh...eee............ee.....hhhhhhhhhhhhh...eeeeee...hhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhh...eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------K-------W--------------------------A--------------------------------------I-------------------------------------------------------------------------A------------------------------N----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yk5 A  49 PVNLIFCYTILQmKVAERImAQHPGERFYVVLmSENRNEKYDYYFNQIKDKAEWAYFFHLPYGLNKSFNFIPTmAELKVKAmLLPKVKRIYLASLEKVSIAAFLSTYPDAEIKTFDDGTINLIQSSSYLGDEFSVNGTIKRNFARmmIGDWSIAKTRNASDEHYTIFKGLKNImDDGRRKmTYLPLFDASELKAGDETGGTVRILLGSPDKEmKEISEKAAKNFNIQYVAPHPRQTYGLSGVTTLNSPYVIEDYILREIKKNPHTRYEIYTFFSGAALTmKDFPNVHVYALKPASLPEDYWLKPVYALFTQSGIPILTFDDKLVPR 374
                                    58  |     68        78  |     88        98       108       118   |   128 |     138       148       158       168       178       188     ||198       208       218   |   228|      238       248       258  |    268       278       288       298       308       318       328       338       348       358       368      
                                       61-MSE 68-MSE       81-MSE                                  122-MSE 130-MSE                                                         194-MSE                     222-MSE  |                             261-MSE                                                            328-MSE                                          
                                                                                                                                                                            195-MSE                           229-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 2YK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YK5)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (LST_NEIMB | P72097)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LST_NEIMB | P72097: 2yk4 2yk6 2yk7

(-) Related Entries Specified in the PDB File

2yk4 STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST).
2yk6 STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CDP.
2yk7 STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CMP-3F-NEU5AC.