2YA2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CATALYTIC MODULE OF THE MULTI-MODULAR GLYCOGEN-DEGRADING PNEUMOCOCCAL VIRULENCE FACTOR SPUA IN COMPLEX WITH AN INHIBITOR.

Authors :   A. Lammerts Van Bueren, E. Ficko-Blean, B. Pluvinage, J. H. Hehemann M. A. Higgins, L. Deng, A. D. Ogunniyi, U. H. Stroeher, N. E. Warry, R. D. M. Czjzek, J. C. Paton, D. J. Vocadlo, A. B. Boraston

Date :   17 Feb 11 (Deposition) - 20 Apr 11 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.37

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Lammerts Van Bueren, E. Ficko-Blean, B. Pluvinage, J. Hehemann, M. A. Higgins, L. Deng, A. D. Ogunniyi, U. H. Stroeher, N. El Warry, R. D. Burke, M. Czjzek, J. C. Paton, D. J. Vocadlo, A. B. Boraston
The Conformation And Function Of A Multimodular Glycogen-Degrading Pneumococcal Virulence Factor.
Structure V. 19 640 2011
PubMed-ID: 21565699 | Reference-DOI: 10.1016/J.STR.2011.03.001

Molecule 1 - PUTATIVE ALKALINE AMYLOPULLULANASE
	Atcc	:	BAA-334D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 436-1143
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	170187
	Strain	:	TIGR4
	Synonym	:	PULLULANASE SPUA GH13

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	NA	1	Ligand/Ion	SODIUM ION
4	NOJ	1	Ligand/Ion	1-DEOXYNOJIRIMYCIN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:210 , TYR A:212 , HIS A:260 , PHE A:288 , ARG A:321 , ASP A:323 , MET A:324 , GLU A:352 , HIS A:439 , ASP A:440 , GLC A:1690	BINDING SITE FOR RESIDUE NOJ A 1689
2	AC2	SOFTWARE	TRP A:210 , TYR A:212 , ASP A:213 , ASP A:534 , ASN A:688 , NOJ A:1689 , HOH A:2179 , HOH A:2206	BINDING SITE FOR RESIDUE GLC A 1690
3	AC3	SOFTWARE	MET A:373 , THR A:376 , ASP A:377 , ASP A:427 , ASP A:431 , HOH A:2148	BINDING SITE FOR RESIDUE CA A 1691
4	AC4	SOFTWARE	LEU A:442 , HOH A:2157	BINDING SITE FOR RESIDUE NA A 1692

(no "SS Bond" information available for 2YA2)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:394	-	Pro A:395

(no "SAP(SNP)/Variant" information available for 2YA2)

(no "PROSITE Motif" information available for 2YA2)

(no "Exon" information available for 2YA2)

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:708
 aligned with A0A0H2UNG0_S | A0A0H2UNG0 from UniProtKB/TrEMBL  Length:1280

    Alignment length:708
                                   445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135        
        A0A0H2UNG0_S    436 TSWRLKDETYSYDGKLGADLKEEGKQVDLTLWSPSADKVSVVVYDKNDPDKVVGTVALEKGERGTWKQTLDSTNKLGITDFTGYYYQYQIERQGKTVLALDPYAKSLAAWNSDDSKIDDAHKVAKAAFVDPAKLGPQDLTYGKIHNFKTREDAVIYEAHVRDFTSDPAIAKDLTKPFGTFEAFIEKLDYLKDLGVTHIQLLPVLSYYFVNELKNHERLSDYASSNSNYNWGYDPQNYFSLTGMYSSDPKNPEKRIAEFKNLINEIHKRGMGAILDVVYNHTAKVDLFEDLEPNYYHFMDADGTPRTSFGGGRLGTTHHMTKRLLIDSIKYLVDTYKVDGFRFDMMGDHDAASIEEAYKAARALNPNLIMLGEGWRTYAGDENMPTKAADQDWMKHTDTVAVFSDDIRNNLKSGYPNEGQPAFITGGKRDVNTIFKNLIAQPTNFEADSPGDVIQYIAAHDNLTLFDIIAQSIKKDPSKAENYAEIHRRLRLGNLMVLTAQGTPFIHSGQEYGRTKQFRDPAYKTPVAEDKVPNKSHLLRDKDGNPFDYPYFIHDSYDSSDAVNKFDWTKATDGKAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVHLITVPGQNGVEKEDVVIGYQITAPNGDIYAVFVNADEKAREFNLGTAFAHLRNAEVLADENQAGPVGIANPKGLEWTEKGLKLNALTATVLRVSQN 1143
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.....eeeeehhhheeeeeee.....eeeeeee.......eeeeee.ee....eeeeee..............eeeeeeee..eeeee......ee....hhhh..hhhhh...ee..hhhhh..............hhhhh.eeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeee..........hhhh.....................................hhhhhhhhhhhhhhhhh..eeeeee.......hhhhhh................ee..ee.....hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.................hhhhhhhh...eeehhhhhhhhh................eehhhhhhhhh.........hhh.eee........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhh...hhhhh...eeeee.....eeeeeeee......hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhheee...........ee.eeeeeee.....eeeeeee.....eeee....hhhhh..eeee...............eee...eeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ya2 A  -19 TSWRLKDETYSYDGKLGADLKEEGKQVDLTLWSPSADKVSVVVYDKNDPDKVVGTVALEKGERGTWKQTLDSTNKLGITDFTGYYYQYQIERQGKTVLALDPYAKSLAAWNSDDSKIDDAHKVAKAAFVDPAKLGPQDLTYGKIHNFKTREDAVIYEAHVRDFTSDPAIAKDLTKPFGTFEAFIEKLDYLKDLGVTHIQLLPVLSYYFVNELKNHERLSDYASSNSNYNWGYDPQNYFSLTGMYSSDPKNPEKRIAEFKNLINEIHKRGMGAILDVVYNHTAKVDLFEDLEPNYYHFMDADGTPRTSFGGGRLGTTHHMTKRLLIDSIKYLVDTYKVDGFRFDMMGDHDAASIEEAYKAARALNPNLIMLGEGWRTYAGDENMPTKAADQDWMKHTDTVAVFSDDIRNNLKSGYPNEGQPAFITGGKRDVNTIFKNLIAQPTNFEADSPGDVIQYIAAHDDLTLFDIIAQSIKKDPSKAENYAEIHRRLRLGNLMVLTAQGTPFIHSGQEYGRTKQFRNPAYRTPVAEDKVPNKSHLLRDKDGNPFDYPYFIHDSYDSSDAVNKFDWTKATDGKAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVHLITVPGQNGVEKEDVVIGYQITAPNGDIYAVFVNADEKAREFNLGTAFAHLRNAEVLADENQAGPVGIANPKGLEWTEKGLKLNALTATVLRVSQN  688
                                   -10         0        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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680

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 2YA2)

(no "CATH Domain" information available for 2YA2)

(no "Pfam Domain" information available for 2YA2)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2YA2)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NOJ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:394 - Pro A:395	[ RasMol ]

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	2ya2
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		Domain Information	:	XDom
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UniProtKB/TrEMBL
	A0A0H2UNG0_S \| A0A0H2UNG0	:	2j44 2ya0 2ya1

2j44	ALPHA-GLUCAN BINDING BY A STREPTOCOCCAL VIRULENCE FACTOR
2ya0	CATALYTIC MODULE OF THE MULTI-MODULAR GLYCOGEN-DEGRADING PNEUMOCOCCAL VIRULENCE FACTOR SPUA
2ya1	PRODUCT COMPLEX OF A MULTI-MODULAR GLYCOGEN-DEGRADING PNEUMOCOCCAL VIRULENCE FACTOR SPUA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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