2W1S - 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)

Title :   UNIQUE LIGAND BINDING SPECIFICITY OF A FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS

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 :   1.45

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

Keywords :   Hexosaminidase, Clostridium Perfringens, Family 32 Carbohydrate Binding Module, Toxin, Secreted, Virulence, Hydrolase, Glycosidase, Family 84 Glycoside 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
	EC Number	:	3.2.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)STAR
	Expression System Taxid	:	469008
	Fragment	:	FAMILY 32 CBM, RESIDUES 807-975
	Organism Scientific	:	CLOSTRIDIUM PERFRINGENS
	Organism Taxid	:	1502
	Synonym	:	FAMILY 84 GLYCOSIDE HYDROLASE, MU TOXIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CA	2	Ligand/Ion	CALCIUM ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
4	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:825 , ASP A:828 , ASP A:830 , THR A:833 , SER A:939 , GLU A:940	BINDING SITE FOR RESIDUE CA A1946
2	AC2	SOFTWARE	ASN B:825 , ASP B:828 , ASP B:830 , THR B:833 , SER B:939 , GLU B:940	BINDING SITE FOR RESIDUE CA B1946
3	AC3	SOFTWARE	ASN A:871 , LYS A:908 , HOH A:2041	BINDING SITE FOR RESIDUE NA A1947
4	AC4	SOFTWARE	TYR A:886 , HOH A:2182 , GLU B:814 , HOH B:2053	BINDING SITE FOR RESIDUE NA B1947
5	AC5	SOFTWARE	TRP A:836 , ASP A:877 , TRP A:935 , HOH A:2121 , HOH A:2262 , HOH A:2263 , HOH A:2264 , HOH A:2265 , TRP B:836 , ASP B:877 , ASN B:933 , LYS B:934 , TRP B:935	BINDING SITE FOR RESIDUE BTB A1948

(no "SS Bond" information available for 2W1S)

(no "Cis Peptide Bond" information available for 2W1S)

Asymmetric Unit (1, 2)

								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	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)

(no "PROSITE Motif" information available for 2W1S)

(no "Exon" information available for 2W1S)

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
                 2w1s A 807 NPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNmENINKWLTFSEFAIVS 945
                                   816       826       836       846       856       866       876       886       896       906       916       926  |    936         
                                                                                                                                                    929-MSE

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with NAGH_CLOPE | P26831 from UniProtKB/Swiss-Prot  Length:1628

    Alignment length:138
                                   817       827       837       847       857       867       877       887       897       907       917       927       937        
           NAGH_CLOPE   808 PSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIIS 945
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -F5_F8_type_C-2w1sB01 B:809-941                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) -F5_F8_type_C-2w1sB02 B:809-941                                                                                                       ---- Pfam domains (2)
         Sec.struct. author .eeee....eeeee.hhhhh.......eeeehhhhhh.....eeeeeeeeeeeeeeeeeee............eeeeeee......eeeeeee........eeeeeeeeeeeeeeeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------V- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w1s B 808 PSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNmENINKWLTFSEFAIVS 945
                                   817       827       837       847       857       867       877       887       897       907       917       927 |     937        
                                                                                                                                                   929-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 '\|'

(no "SCOP Domain" information available for 2W1S)

(no "CATH Domain" information available for 2W1S)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: F5_F8_type_C (45)

Clostridium perfringens (5)

1a	F5_F8_type_C-2w1sB01	B:809-941
1b	F5_F8_type_C-2w1sB02	B:809-941

Asymmetric Unit(hide GO term definitions)

Chain A,B (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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BTB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w1s)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2w1s
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NAGH_CLOPE \| P26831
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.35
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NAGH_CLOPE \| P26831
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

2w1q	UNIQUE LIGAND BINDING SPECIFICITY FOR A FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS
2w1u	A FAMILY 32 CARBOHYDRATE-BINDING MODULE, FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH BETA-D-GLCNAC- BETA1-3GALNAC
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 (4, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File