2YK6 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CDP.

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) - 02 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.83

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Transferase, Lipooligosaccharide Sialyltransferase (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

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CDP	1	Ligand/Ion	CYTIDINE-5'-DIPHOSPHATE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CDP	2	Ligand/Ion	CYTIDINE-5'-DIPHOSPHATE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:59 , ASN A:117 , PHE A:118 , LEU A:254 , GLY A:255 , ALA A:278 , PRO A:279 , HIS A:280 , PRO A:281 , ARG A:282 , VAL A:298 , ILE A:299 , GLU A:300 , SER A:322 , GLY A:323 , ALA A:324 , HOH A:2025 , HOH A:2059	BINDING SITE FOR RESIDUE CDP A1374
2	AC2	SOFTWARE	MET A:81 , ASN 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:2010	BINDING SITE FOR RESIDUE 1PE A1375
3	AC3	SOFTWARE	GLY A:178 , ASP A:179 , GLU A:180 , SER A:288 , GLY A:289	BINDING SITE FOR RESIDUE SO4 A1376

(no "SS Bond" information available for 2YK6)

(no "Cis Peptide Bond" information available for 2YK6)

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LST_NEIMB_004 *	N	94	K	LST_NEIMB	---	---	A	N	94	K
2	UniProt	VAR_LST_NEIMB_005 *	R	102	W	LST_NEIMB	---	---	A	W	102	W
3	UniProt	VAR_LST_NEIMB_006 *	S	129	A	LST_NEIMB	---	---	A	A	129	A
4	UniProt	VAR_LST_NEIMB_007 *	G	168	I	LST_NEIMB	---	---	A	I	168	I
5	UniProt	VAR_LST_NEIMB_008 *	T	242	A	LST_NEIMB	---	---	A	A	242	A
6	UniProt	VAR_LST_NEIMB_009 *	K	273	N	LST_NEIMB	---	---	A	N	273	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LST_NEIMB_004 *	N	94	K	LST_NEIMB	---	---	A	N	94	K
2	UniProt	VAR_LST_NEIMB_005 *	R	102	W	LST_NEIMB	---	---	A	W	102	W
3	UniProt	VAR_LST_NEIMB_006 *	S	129	A	LST_NEIMB	---	---	A	A	129	A
4	UniProt	VAR_LST_NEIMB_007 *	G	168	I	LST_NEIMB	---	---	A	I	168	I
5	UniProt	VAR_LST_NEIMB_008 *	T	242	A	LST_NEIMB	---	---	A	A	242	A
6	UniProt	VAR_LST_NEIMB_009 *	K	273	N	LST_NEIMB	---	---	A	N	273	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2YK6)

(no "Exon" information available for 2YK6)

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:325
 aligned with LST_NEIMB | P72097 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:325
                                                                                                                                                                                                                                                                                                                                                            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...hhhhhhhhhhhhh...eeeeee.............hhhhhhhhhh......eeeee.hhhhhhhhhhhh....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
                 2yk6 A  49 PVNLIFCYTILQMKVAERIMAQHPGERFYVVLMSENRNEKYDYYFNQIKDKAEWAYFFHLPYGLNKSFNFIPTMAELKVKAMLLPKVKRIYLASLEKVSIAAFLSTYPDAEIKTFDDGTINLIQSSSYLGDEFSVNGTIKRNFARMMIGDWSIAKTRNASDEHYTIFKGLKNIMDDGRRKMTYLPLFDASELKAGDETGGTVRILLGSPDKEMKEISEKAAKNFNIQYVAPHPRQTYGLSGVTTLNSPYVIEDYILREIKKNPHTRYEIYTFFSGAALTMKDFPNVHVYALKPASLPEDYWLKPVYALFTQSGIPILTFDDKLVP 373
                                    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

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 '\|'

(no "SCOP Domain" information available for 2YK6)

(no "CATH Domain" information available for 2YK6)

(no "Pfam Domain" information available for 2YK6)

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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yk6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2yk6
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	2.4.99.-
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UniProtKB/Swiss-Prot
	LST_NEIMB \| P72097	:	2yk4 2yk5 2yk7

2yk4	STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST).
2yk5	STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CMP.
2yk7	STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CMP-3F-NEU5AC.

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

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