2J7M - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CHARACTERIZATION OF A FAMILY 32 CBM

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

Date :   12 Oct 06 (Deposition) - 16 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Glycoside Hydrolase, Carbohydrate Binding, Cbm, Hydrolase, H-Trisaccharide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ficko-Blean, A. B. Boraston
The Interaction Of A Carbohydrate-Binding Module From A Clostridium Perfringens N-Acetyl-Beta- Hexosaminidase With Its Carbohydrate Receptor
J. Biol. Chem. V. 281 37748 2006
PubMed-ID: 16990278 | Reference-DOI: 10.1074/JBC.M606126200

Molecule 1 - HYALURONIDASE
	Atcc	:	13124
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 625-767
	Organism Scientific	:	CLOSTRIDIUM PERFRINGENS
	Organism Taxid	:	1502
	Synonym	:	CBM32

		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	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:695 , ASP A:749 , GLN A:750 , GAL A:1770 , FUC A:1771 , HOH A:2204 , HOH A:2205	BINDING SITE FOR RESIDUE NDG A1769
2	AC2	SOFTWARE	GLU A:641 , HIS A:658 , ARG A:690 , ASN A:695 , GLN A:750 , PHE A:757 , NDG A:1769 , FUC A:1771 , HOH A:2207 , HOH A:2208	BINDING SITE FOR RESIDUE GAL A1770
3	AC3	SOFTWARE	ARG A:690 , NDG A:1769 , GAL A:1770 , HOH A:2113 , HOH A:2180 , HOH A:2209	BINDING SITE FOR RESIDUE FUC A1771
4	AC4	SOFTWARE	PHE A:647 , ASP A:650 , ASP A:652 , THR A:655 , ALA A:761	BINDING SITE FOR RESIDUE CA A1768

(no "SS Bond" information available for 2J7M)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:663	-	Pro A:664
2	Gly A:668	-	Pro A:669

(no "SAP(SNP)/Variant" information available for 2J7M)

(no "PROSITE Motif" information available for 2J7M)

(no "Exon" information available for 2J7M)

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:143
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:143
                                   634       644       654       664       674       684       694       704       714       724       734       744       754       764   
            OGA_CLOP1   625 NPRTVKITASSEETSGENAPASFASDGDMNTFWHSKWSSPAHEGPHHLTLELDNVYEINKVKYAPRQDSKNGRITGYKVSVSLDGENFTEVKTGTLEDNAAIKFIEFDSVDAKYVRLDVTDSVSDQANGRGKFATAAEVNVHG 767
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..........hhhhhhh......ee...........eeeeeeeeeeeeeeeeeee.........eeeeeeeee.....eeeeeeee.......eeeeeeeeeeeeeeeeeeee............ee.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j7m A 625 NPRTVKITASSEETSGENAPASFASDGDMNTFWHSKWSSPAHEGPHHLTLELDNVYEINKVKYAPRQDSKNGRITGYKVSVSLDGENFTEVKTGTLEDNAAIKFIEFDSVDAKYVRLDVTDSVSDQANGRGKFATAAEVNVHG 767
                                   634       644       654       664       674       684       694       704       714       724       734       744       754       764

Chain A from PDB  Type:PROTEIN  Length:143
 aligned with OGA_CLOPE | Q8XL08 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:143
                                   634       644       654       664       674       684       694       704       714       724       734       744       754       764   
            OGA_CLOPE   625 NPRTVKITASSEETSGENAPASFASDGDMNTFWHSKWSSPAHEGPHHLTLELDNVYEINKVKYAPRQDSKNGRITGYKVSVSLDGENFTEVKTGTLEDNAAIKFIEFDSVDAKYVRLDVTDSVSDQANGRGKFATAAEVNVHG 767
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..........hhhhhhh......ee...........eeeeeeeeeeeeeeeeeee.........eeeeeeeee.....eeeeeeee.......eeeeeeeeeeeeeeeeeeee............ee.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j7m A 625 NPRTVKITASSEETSGENAPASFASDGDMNTFWHSKWSSPAHEGPHHLTLELDNVYEINKVKYAPRQDSKNGRITGYKVSVSLDGENFTEVKTGTLEDNAAIKFIEFDSVDAKYVRLDVTDSVSDQANGRGKFATAAEVNVHG 767
                                   634       644       654       664       674       684       694       704       714       724       734       744       754       764

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 2J7M)

(no "CATH Domain" information available for 2J7M)

(no "Pfam Domain" information available for 2J7M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OGA_CLOP1 | Q0TR53)

molecular function
	GO:0016231	beta-N-acetylglucosaminidase activity	Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
	GO:0004563	beta-N-acetylhexosaminidase activity	Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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:0006517	protein deglycosylation	The removal of sugar residues from a glycosylated protein.

Chain A (OGA_CLOPE | Q8XL08)

molecular function
	GO:0004563	beta-N-acetylhexosaminidase activity	Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:668 - Pro A:669	[ RasMol ]
		Ser A:663 - Pro A:664	[ RasMol ]

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2cbi	STRUCTURE OF THE CLOSTRIDIUM PERFRINGENS NAGJ FAMILY 84 GLYCOSIDE HYDROLASE, A HOMOLOGUE OF HUMAN O-GLCNACASE
2cbj	STRUCTURE OF THE CLOSTRIDIUM PERFRINGENS NAGJ FAMILY 84 GLYCOSIDE HYDROLASE, A HOMOLOGUE OF HUMAN O-GLCNACASE IN COMPLEX WITH PUGNAC
2j1a	STRUCTURE OF CBM32 FROM CLOSTRIDIUM PERFRINGENS BETA-N-ACETYLHEXOSAMINIDASE GH84C IN COMPLEX WITH GALACTOSE
2j1e	HIGH RESOLUTION CRYSTAL STRUCTURE OF CBM32 FROM A N-ACETYL-BETA-HEXOSAMINIDASE IN COMPLEX WITH LACNAC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 13)

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