2W1U - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   A FAMILY 32 CARBOHYDRATE-BINDING MODULE, FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH BETA-D-GLCNAC-BETA(1,3)GALNAC

Authors :   E. Ficko-Blean, A. B. Boraston

Date :   20 Oct 08 (Deposition) - 05 May 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Family 32 Carbohydrate Binding Module, Family 84 Glycoside Hydrolase, Glycosidase, Hexosaminidase, Clostridium Perfringens, Cbm, Toxin, Secreted, Virulence, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ficko-Blean, A. B. Boraston
N-Acetylglucosamine Recognition By A Family 32 Carbohydrate-Binding Module From Clostridium Perfringens Nagh.
J. Mol. Biol. V. 390 208 2009
PubMed-ID: 19422833 | Reference-DOI: 10.1016/J.JMB.2009.04.066

Molecule 1 - HYALURONOGLUCOSAMINIDASE
	Atcc	:	13124
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Fragment	:	FAMILY 32 CBM, RESIDUES 807-975
	Organism Scientific	:	CLOSTRIDIUM PERFRINGENS
	Organism Taxid	:	1502
	Synonym	:	FAMILY 84 GLYCOSIDE HYDROLASE, MU TOXIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	ACT	3	Ligand/Ion	ACETATE ION
3	CA	4	Ligand/Ion	CALCIUM ION
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NGA	3	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	A2G	-1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	ACT	-1	Ligand/Ion	ACETATE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	A2G	-1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	ACT	1	Ligand/Ion	ACETATE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	ACT	1	Ligand/Ion	ACETATE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NGA	-1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	A2G	-1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	ACT	1	Ligand/Ion	ACETATE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:819 , TRP A:836 , ASP A:877 , ASN A:933 , LYS A:934 , TRP A:935 , NGA A:1947 , HOH A:2152	BINDING SITE FOR RESIDUE NAG A1946
02	AC2	SOFTWARE	ASP A:843 , NAG A:1946 , HOH A:2154 , ASP D:828 , GLY D:829	BINDING SITE FOR RESIDUE NGA A1947
03	AC3	SOFTWARE	TYR B:819 , TRP B:836 , ASP B:877 , ASN B:933 , LYS B:934 , TRP B:935 , NGA B:1951 , HOH B:2165 , HOH B:2166 , HOH B:2167 , HOH B:2170	BINDING SITE FOR RESIDUE NAG B1950
04	AC4	SOFTWARE	TYR B:819 , ASP B:843 , NAG B:1950 , HOH B:2169 , HOH B:2170	BINDING SITE FOR RESIDUE NGA B1951
05	AC5	SOFTWARE	TYR C:819 , TRP C:836 , ASP C:877 , ASN C:933 , LYS C:934 , TRP C:935 , A2G C:1949 , HOH C:2189 , HOH C:2190 , HOH C:2192 , HOH C:2196	BINDING SITE FOR RESIDUE NAG C1948
06	AC6	SOFTWARE	ASP B:828 , GLY B:829 , ASP B:830 , ASP C:843 , NAG C:1948 , HOH C:2066 , HOH C:2193 , HOH C:2194 , HOH C:2195 , HOH C:2196	BINDING SITE FOR RESIDUE A2G C1949
07	AC7	SOFTWARE	TYR D:819 , TRP D:836 , ASP D:877 , ASN D:933 , LYS D:934 , TRP D:935 , NGA D:1949 , HOH D:2174	BINDING SITE FOR RESIDUE NAG D1948
08	AC8	SOFTWARE	ASP D:843 , NAG D:1948 , HOH D:2175 , HOH D:2176	BINDING SITE FOR RESIDUE NGA D1949
09	AC9	SOFTWARE	ASN D:825 , ASP D:828 , ASP D:830 , THR D:833 , SER D:939 , GLU D:940	BINDING SITE FOR RESIDUE CA D1950
10	BC1	SOFTWARE	ASN A:825 , ASP A:828 , ASP A:830 , THR A:833 , SER A:939 , GLU A:940	BINDING SITE FOR RESIDUE CA A1948
11	BC2	SOFTWARE	ASN B:825 , ASP B:828 , ASP B:830 , THR B:833 , SER B:939 , GLU B:940	BINDING SITE FOR RESIDUE CA B1952
12	BC3	SOFTWARE	ASN C:825 , ASP C:828 , ASP C:830 , THR C:833 , SER C:939 , GLU C:940	BINDING SITE FOR RESIDUE CA C1950
13	BC4	SOFTWARE	ALA B:824 , ASN B:825 , ASP B:828 , GLN C:817 , VAL C:818 , TYR C:819 , LYS C:838	BINDING SITE FOR RESIDUE ACT C1951
14	BC5	SOFTWARE	LYS A:897 , GLU A:913 , LYS D:883 , THR D:895 , MET D:929 , HOH D:2178 , HOH D:2179	BINDING SITE FOR RESIDUE ACT D1951
15	BC6	SOFTWARE	LEU B:855 , ILE B:859 , LEU B:948 , HOH B:2011	BINDING SITE FOR RESIDUE ACT B1953

(no "SS Bond" information available for 2W1U)

(no "Cis Peptide Bond" information available for 2W1U)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NAGH_CLOPE_006 *	I	944	V	NAGH_CLOPE	---	---	A/B/C/D	V	944	V
	* ID not provided by source

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NAGH_CLOPE_006 *	I	944	V	NAGH_CLOPE	---	---	A	V	944	V
	* ID not provided by source

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NAGH_CLOPE_006 *	I	944	V	NAGH_CLOPE	---	---	B	V	944	V
	* ID not provided by source

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NAGH_CLOPE_006 *	I	944	V	NAGH_CLOPE	---	---	C	V	944	V
	* ID not provided by source

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NAGH_CLOPE_006 *	I	944	V	NAGH_CLOPE	---	---	D	V	944	V
	* ID not provided by source

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

(no "PROSITE Motif" information available for 2W1U)

(no "Exon" information available for 2W1U)

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:139
 aligned with NAGH_CLOPE | P26831 from UniProtKB/Swiss-Prot  Length:1628

    Alignment length:139
                                   816       826       836       846       856       866       876       886       896       906       916       926       936         
           NAGH_CLOPE   807 NPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIIS 945
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eeeee.hhhhh.......eeeehhhhhh.....eeeeeeeeeeeeeeeeeee............eeeeeee......eeeeeee........eeeeeeeeeeeeeeeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------V- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w1u A 807 NPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIVS 945
                                   816       826       836       846       856       866       876       886       896       906       916       926       936

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with NAGH_CLOPE | P26831 from UniProtKB/Swiss-Prot  Length:1628

    Alignment length:146
                                   813       823       833       843       853       863       873       883       893       903       913       923       933       943      
           NAGH_CLOPE   804 VEFNPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIISDELE 949
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....eeeee.hhhhh.......eeeehhhhhh.....eeeeeeeeeeeeeeeeeee............eeeeeee......eeeeeee........eeeeeeeeeeeeeeeeeeee.......eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------V----- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w1u B 804 MASNPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIVSDELE 949
                                   813       823       833       843       853       863       873       883       893       903       913       923       933       943

Chain C from PDB  Type:PROTEIN  Length:140
 aligned with NAGH_CLOPE | P26831 from UniProtKB/Swiss-Prot  Length:1628

    Alignment length:140
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947
           NAGH_CLOPE   808 PSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIISDE 947
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeee.hhhhhh.......eeeehhhhhh.....eeeeeeeeeeeeeeeeeee............eeeeeee......eeeeeee........eeeeeeeeeeeeeeeeeeee.......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------V--- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w1u C 808 PSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIVSDE 947
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with NAGH_CLOPE | P26831 from UniProtKB/Swiss-Prot  Length:1628

    Alignment length:144
                                   813       823       833       843       853       863       873       883       893       903       913       923       933       943    
           NAGH_CLOPE   804 VEFNPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIISDE 947
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----F5_F8_type_C-2w1uD01 D:809-941                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) -----F5_F8_type_C-2w1uD02 D:809-941                                                                                                       ------ Pfam domains (2)
           Pfam domains (3) -----F5_F8_type_C-2w1uD03 D:809-941                                                                                                       ------ Pfam domains (3)
           Pfam domains (4) -----F5_F8_type_C-2w1uD04 D:809-941                                                                                                       ------ Pfam domains (4)
         Sec.struct. author .....eeee....eeeee.hhhhh.......eeee...........eeeeeeeeeeeeeeeeeee............eeeeeee......eeeeeee........eeeeeeeeeeeeeeeeeeee.......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------V--- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w1u D 804 MASNPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIVSDE 947
                                   813       823       833       843       853       863       873       883       893       903       913       923       933       943

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 2W1U)

(no "CATH Domain" information available for 2W1U)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: F5_F8_type_C (45)

Clostridium perfringens (5)

1a	F5_F8_type_C-2w1uD01	D:809-941
1b	F5_F8_type_C-2w1uD02	D:809-941
1c	F5_F8_type_C-2w1uD03	D:809-941
1d	F5_F8_type_C-2w1uD04	D:809-941

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NAGH_CLOPE | P26831)

molecular function
	GO:0004415	hyalurononglucosaminidase activity	Catalysis of the random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w1u)

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		Biological Unit 4	[ Jena3D ]

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	2w1u
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	NAGH_CLOPE \| P26831
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UniProtKB/Swiss-Prot
	NAGH_CLOPE \| P26831	:	2jnk 2ozn 2w1q 2w1s 2wdb

2w1q	UNIQUE LIGAND BINDING SPECIFICITY FOR A FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS
2w1s	UNIQUE LIGAND BINDING SPECIFICITY OF A FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS
2wdb	A FAMILY 32 CARBOHYDRATE-BINDING MODULE, FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH BETA-D-GLCNAC- BETA(1,2)MANNOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (7, 7)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File