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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE TYPE I DOCKERIN DOMAIN FROM THE CLOSTRIDIUM THERMOCELLUM CELLULOSOME (20 STRUCTURES)

Authors :   B. L. Lytle, B. F. Volkman, W. M. Westler, M. P. Heckman, J. H. D. Wu

Date :   31 Oct 99 (Deposition) - 04 Apr 01 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Cellulose Degradation, Cellulosome, Calcium-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. L. Lytle, B. F. Volkman, W. M. Westler, M. P. Heckman, J. H. D. Wu
Solution Structure Of A Type I Dockerin Domain, A Novel Prokaryotic, Extracellular Calcium-Binding Domain.
J. Mol. Biol. V. 307 745 2001
PubMed-ID: 11273698 | Reference-DOI: 10.1006/JMBI.2001.4522
(for further references see the PDB file header)

Molecule 1 - ENDOGLUCANASE SS
	Chains	:	A
	EC Number	:	3.2.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCYB2
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TYPE I DOCKERIN DOMAIN (RESIDUES 673-741)
	Organism Scientific	:	CLOSTRIDIUM THERMOCELLUM
	Organism Taxid	:	1515
	Synonym	:	CELS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

NMR Structure (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , ASN A:10 , ASP A:12 , GLY A:13 , LYS A:14 , ASP A:19	BINDING SITE FOR RESIDUE CA A 72
2	AC2	SOFTWARE	ASP A:40 , ASN A:42 , ASP A:44 , ARG A:46 , ASP A:51	BINDING SITE FOR RESIDUE CA A 73
3	I	AUTHOR	ASP A:8 , VAL A:9 , ASN A:10 , ASP A:11 , ASP A:12 , GLY A:13 , LYS A:14 , VAL A:15 , ASN A:16 , SER A:17 , THR A:18 , ASP A:19	FIRST PREDICTED CA2+ BINDING LOOP
4	II	AUTHOR	ASP A:40 , LEU A:41 , ASN A:42 , GLU A:43 , ASP A:44 , GLY A:45 , ARG A:46 , VAL A:47 , ASN A:48 , SER A:49 , THR A:50 , ASP A:51	SECOND PREDICTED CA2+ BINDING LOOP

(no "SS Bond" information available for 1DAV)

(no "Cis Peptide Bond" information available for 1DAV)

(no "SAP(SNP)/Variant" information available for 1DAV)

NMR Structure (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DOCKERIN	PS51766	Dockerin domain profile.	GUNS_CLOTH	673-739	1	A:2-68
1	DOCKERIN	PS51766	Dockerin domain profile.	GUNS_CLOTM	673-739	1	A:2-68
2	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	GUNS_CLOTH	679-698 711-730	2	A:8-27 A:40-59
2	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	GUNS_CLOTM	679-698 711-730	2	A:8-27 A:40-59

(no "Exon" information available for 1DAV)

NMR Structure

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:71
 aligned with GUNS_CLOTH | A3DH67 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:89
                                                                                                                 741 
                                   663       673       683       693       703       713       723       733       | 
           GUNS_CLOTH   654 MGVLATYFPDMTYKVPGTPSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKN-   -
               SCOP domains d                  1dava_ A: Cellulosome endoglucanase SS                                 SCOP domains
               CATH domains 1                  davA00 A:1-71 Type 1 dockerin domain                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------------.................hhhhhhhhhhh......hhhh...........hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------DOCKERIN  PDB: A:2-68 UniProt: 673-739                             --- PROSITE (2)
                PROSITE (3) -------------------------CLOS_CELLULOSOME_RPT------------CLOS_CELLULOSOME_RPT------------ PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1dav A   1 M------------------STKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG  71
                            |        -         2        12        22        32        42        52        62         
                            |                  2                                                                     
                            1

Chain A from PDB  Type:PROTEIN  Length:71
 aligned with GUNS_CLOTM | P0C2S5 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:89
                                                                                                                 741 
                                   663       673       683       693       703       713       723       733       | 
           GUNS_CLOTM   654 MGVLATYFPDMTYKVPGTPSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKN-   -
               SCOP domains d                  1dava_ A: Cellulosome endoglucanase SS                                 SCOP domains
               CATH domains 1                  davA00 A:1-71 Type 1 dockerin domain                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------------.................hhhhhhhhhhh......hhhh...........hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------DOCKERIN  PDB: A:2-68 UniProt: 673-739                             --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------CLOS_CELLULOSOME_RPT------------CLOS_CELLULOSOME_RPT------------ PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1dav A   1 M------------------STKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG  71
                            |        -         2        12        22        32        42        52        62         
                            1                  2

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Type I dockerin domain (11)

Superfamily: Type I dockerin domain (11)

Family: Type I dockerin domain (6)

Protein domain: Cellulosome endoglucanase SS (2)

Clostridium thermocellum [TaxId: 1515] (2)

d1dava_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Type 1 dockerin domain (2)

Homologous Superfamily: Type 1 dockerin domain (2)

Clostridium thermocellum. Organism_taxid: 1515. (2)

1davA00

A:1-71

(no "Pfam Domain" information available for 1DAV)

NMR Structure(hide GO term definitions)

Chain A (GUNS_CLOTM | P0C2S5)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0008810	cellulase activity	Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
	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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	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.

Chain A (GUNS_CLOTH | A3DH67)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0008810	cellulase activity	Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
	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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	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.

NMR Structure
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1daq	MINIMIZED AVERAGE STRUCTURE

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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