2VZQ - JenaLib

Title :   C-TERMINAL CBM35 FROM AMYCOLATOPSIS ORIENTALIS EXO-CHITOSANASE CSXA IN COMPLEX WITH DIGALACTURONIC ACID

Authors :   A. Lammerts Van Bueren, A. B. Boraston

Date :   05 Aug 08 (Deposition) - 13 Jan 09 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Hydrolase, Cbm, Family 35, Digalacturonic Acid, Calcium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Montanier, A. L. Van Bueren, C. Dumon, J. E. Flint, M. A. Correia, J. A. Prates, S. J. Firbank, R. J. Lewis, G. G. Grondin, M. G. Ghinet, T. M. Gloster, C. Herve, J. P. Knox, B. G. Talbot, J. P. Turkenburg, J. Kerovuo, R. Brzezinski, C. M. G. A. Fontes, G. J. Davies, A. B. Boraston, H. J. Gilbert
Evidence That Family 35 Carbohydrate Binding Modules Displa Conserved Specificity But Divergent Function.
Proc. Natl. Acad. Sci. Usa V. 106 3065 2009
PubMed-ID: 19218457 | Reference-DOI: 10.1073/PNAS.0808972106

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:22 , ASN A:32 , ASN A:35 , ARG A:67 , TRP A:90 , ASN A:121 , CA A:1130 , HOH A:2056 , HOH A:2058 , HOH A:2086 , HOH A:2216 , HOH A:2217 , HOH A:2218 , HOH A:2219	BINDING SITE FOR RESIDUE UNF A 1128
02	AC2	SOFTWARE	GLN A:7 , GLU A:9 , THR A:26 , GLY A:29 , ASP A:123	BINDING SITE FOR RESIDUE CA A 1129
03	AC3	SOFTWARE	GLN B:7 , GLU B:9 , THR B:26 , GLY B:29 , ASP B:123	BINDING SITE FOR RESIDUE CA B 1128
04	AC4	SOFTWARE	ASN B:32 , TYR B:33 , ASN B:35 , UNF B:1133 , HOH B:2102 , HOH B:2225 , HOH B:2227	BINDING SITE FOR RESIDUE CA B 1129
05	AC5	SOFTWARE	ASN A:32 , TYR A:33 , ASN A:35 , UNF A:1128 , HOH A:2086 , HOH A:2204 , HOH A:2206	BINDING SITE FOR RESIDUE CA A 1130
06	AC6	SOFTWARE	ASN B:21 , UNF B:1133 , HOH B:2064	BINDING SITE FOR RESIDUE NA B 1134
07	AC7	SOFTWARE	THR A:52 , SER A:78 , ARG A:99 , THR A:101 , HOH A:2156 , HOH A:2220 , HOH A:2221	BINDING SITE FOR RESIDUE EDO A 1131
08	AC8	SOFTWARE	SER A:78	BINDING SITE FOR RESIDUE EDO A 1132
09	AC9	SOFTWARE	ALA B:23 , GLY B:24 , TYR B:25 , HOH B:2237 , HOH B:2238	BINDING SITE FOR RESIDUE EDO B 1130
10	BC1	SOFTWARE	VAL B:73 , SER B:76 , ILE B:77 , SER B:78 , THR B:101 , EDO B:1132	BINDING SITE FOR RESIDUE EDO B 1131
11	BC2	SOFTWARE	THR B:52 , SER B:78 , ARG B:99 , THR B:101 , EDO B:1131 , HOH B:2240	BINDING SITE FOR RESIDUE EDO B 1132
12	BC3	SOFTWARE	HIS B:22 , ASN B:32 , ASN B:35 , ARG B:67 , TRP B:90 , ASN B:121 , CA B:1129 , NA B:1134 , HOH B:2064 , HOH B:2065 , HOH B:2102 , HOH B:2242 , HOH B:2243 , HOH B:2244 , HOH B:2245	BINDING SITE FOR RESIDUE UNF B 1133

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:126
 aligned with EBDG_AMYOR | Q56F26 from UniProtKB/Swiss-Prot  Length:1032

    Alignment length:126
                                   916       926       936       946       956       966       976       986       996      1006      1016      1026      
          EBDG_AMYOR    907 DPVDYQAEDATIVQGAVESNHAGYTGTGFVNYDNVAGSSVEWTVTVPSAGTYDVVVRYANGTTTSRPLDFSVNGSISASGVAFGSTGTWPAWTTKTVRVTLAAGVNKIKAVATTANGGPNVDKITL 1032
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.hhheee.eeee..........eeee......eeeeeeee...eeeeeeeeee........eeeee..eeeeeee...........eeeeeeeee..eeeeeeeee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --CBM6  PDB: A:4-127 UniProt: 909-1032                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                2vzq A    2 DPVDYQAEDATIVQGAVESNHAGYTGTGFVNYDNVAGSSVEWTVTVPSAGTYDVVVRYANGTTTSRPLDFSVNGSISASGVAFGSTGTWPAWTTKTVRVTLAAGVNKIKAVATTANGGPNVDKITL  127
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with EBDG_AMYOR | Q56F26 from UniProtKB/Swiss-Prot  Length:1032

    Alignment length:126
                                   916       926       936       946       956       966       976       986       996      1006      1016      1026      
          EBDG_AMYOR    907 DPVDYQAEDATIVQGAVESNHAGYTGTGFVNYDNVAGSSVEWTVTVPSAGTYDVVVRYANGTTTSRPLDFSVNGSISASGVAFGSTGTWPAWTTKTVRVTLAAGVNKIKAVATTANGGPNVDKITL 1032
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----CBM_6-2vzqB01 B:7-127                                                                                                     Pfam domains (1)
           Pfam domains (2) -----CBM_6-2vzqB02 B:7-127                                                                                                     Pfam domains (2)
         Sec.struct. author ..eeee.hhheee.eeee..........eeee......eeeeeeee...eeeeeeeeee........eeeee..eeeeeee...........eeeeeeeee..eeeeeeeee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --CBM6  PDB: B:4-127 UniProt: 909-1032                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                2vzq B    2 DPVDYQAEDATIVQGAVESNHAGYTGTGFVNYDNVAGSSVEWTVTVPSAGTYDVVVRYANGTTTSRPLDFSVNGSISASGVAFGSTGTWPAWTTKTVRVTLAAGVNKIKAVATTANGGPNVDKITL  127
                                    11        21        31        41        51        61        71        81        91       101       111       121

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (EBDG_AMYOR | Q56F26)

molecular function
	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:0052761	exo-1,4-beta-D-glucosaminidase activity	Catalysis of the reaction: [beta-(1->4)-D-glucosamine]n-[N-acetyl-D-glucosamine]m = D-glucosamine + [beta-(1->4)-D-glucosamine](n-1)-[N-acetyl-D-glucosamine]m. This reaction is the hydrolysis of chitosan or chitosan oligosaccharides to remove a D-glucosamine residue from the non-reducing termini; chitosan is a linear polysaccharide composed of randomly distributed beta-(1->4)-linked D-glucosamine and N-acetyl-D-glucosamine units.
	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.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-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:0006032	chitin catabolic process	The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
	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: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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Visualization

Interactive Views

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNF	[ 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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

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

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2vzq
		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
	EBDG_AMYOR \| Q56F26
		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)
	(no 'Enzyme Classificator' available)
		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

Description