2YK4 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST).

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 :   1.94

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

Molecule 1 - CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3- SIALYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.99.-
	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 (4, 16)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	EGC	1	Ligand/Ion	2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 32)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	EGC	2	Ligand/Ion	2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:54 , TYR A:56 , VAL A:79 , TRP A:102 , PHE A:106 , TYR A:110 , LEU A:112 , ASN A:113 , SER A:115 , LEU A:143 , VAL A:146 , SER A:147 , ILE A:148 , ALA A:150 , PHE A:151 , HOH A:2062 , HOH A:2092 , HOH A:2252	BINDING SITE FOR RESIDUE EGC A1374
2	AC2	SOFTWARE	LEU A:59 , VAL A:63 , ASP A:164 , GLY A:166 , ILE A:214 , HOH A:2106 , HOH A:2107	BINDING SITE FOR RESIDUE EDO A1375
3	AC3	SOFTWARE	SER A:322 , GLY A:323 , HOH A:2072 , HOH A:2108 , HOH A:2221	BINDING SITE FOR RESIDUE EDO A1376
4	AC4	SOFTWARE	ALA A:69 , GLN A:70 , ASN A:271 , THR A:366 , PHE A:367 , ASP A:368 , HOH A:2009 , HOH A:2253	BINDING SITE FOR RESIDUE EDO A1377
5	AC5	SOFTWARE	HIS A:71 , GLU A:74 , ARG A:137 , ARG A:251 , ASN A:273	BINDING SITE FOR RESIDUE SO4 A1378

(no "SS Bond" information available for 2YK4)

(no "Cis Peptide Bond" information available for 2YK4)

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 2YK4)

(no "Exon" information available for 2YK4)

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
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Chain A from PDB  Type:PROTEIN  Length:326
 aligned with LST_NEIMB | P72097 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:326
                                                                                                                                                                                                                                                                                                                                                             371  
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367   |  
            LST_NEIMB    48 EPVNLIFCYTILQMKVAERIMAQHPGERFYVVLMSENRNEKYDYYFNQIKDKAERAYFFHLPYGLNKSFNFIPTMAELKVKSMLLPKVKRIYLASLEKVSIAAFLSTYPDAEIKTFDDGTGNLIQSSSYLGDEFSVNGTIKRNFARMMIGDWSIAKTRNASDEHYTIFKGLKNIMDDGRRKMTYLPLFDASELKTGDETGGTVRILLGSPDKEMKEISEKAAKNFKIQYVAPHPRQTYGLSGVTTLNSPYVIEDYILREIKKNPHTRYEIYTFFSGAALTMKDFPNVHVYALKPASLPEDYWLKPVYALFTQSGIPILTFDDKN--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh.eeeeee.............hhhhhhhhhhhh....eeeee.hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeee..............eeee.................eeeeee...hhhhhhhhhhhhhhhh..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
                 2yk4 A  48 EPVNLIFCYTILQmKVAERImAQHPGERFYVVLmSENRNEKYDYYFNQIKDKAEWAYFFHLPYGLNKSFNFIPTmAELKVKAmLLPKVKRIYLASLEKVSIAAFLSTYPDAEIKTFDDGTINLIQSSSYLGDEFSVNGTIKRNFARmmIGDWSIAKTRNASDEHYTIFKGLKNImDDGRRKmTYLPLFDASELKAGDETGGTVRILLGSPDKEmKEISEKAAKNFNIQYVAPHPRQTYGLSGVTTLNSPYVIEDYILREIKKNPHTRYEIYTFFSGAALTmKDFPNVHVYALKPASLPEDYWLKPVYALFTQSGIPILTFDDKLVP 373
                                    57   |    67|       77   |    87        97       107       117    |  127  |    137       147       157       167       177       187      |197       207       217    |  227 |     237       247       257   |   267       277       287       297       307       317       327|      337       347       357       367      
                                        61-MSE 68-MSE       81-MSE                                  122-MSE 130-MSE                                                         194-MSE                     222-MSE  |                             261-MSE                                                            328-MSE                                         
                                                                                                                                                                             195-MSE                           229-MSE

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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 '\|'

(no "SCOP Domain" information available for 2YK4)

(no "CATH Domain" information available for 2YK4)

(no "Pfam Domain" information available for 2YK4)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yk4)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2yk4
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	LST_NEIMB \| P72097	:	2yk5 2yk6 2yk7

2yk5	STRUCTURE OF NEISSERIA LOS-SPECIFIC SIALYLTRANSFERASE (NST), IN COMPLEX WITH CMP.
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.

Description

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Ligands, Modified Residues, Ions (4, 16)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (6, 6)

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