2B59 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE TYPE II COHESIN DOCKERIN COMPLEX

Authors :   J. J. Adams, S. P. Smith, Montreal-Kingston Bacterial Structural G Initiative (Bsgi)

Date :   27 Sep 05 (Deposition) - 11 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein-Protein Complex, Cellulosome, Ef Hand, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Hydrolase-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Adams, G. Pal, Z. Jia, S. P. Smith
Mechanism Of Bacterial Cell-Surface Attachment Revealed By The Structure Of Cellulosomal Type Ii Cohesin-Dockerin Complex.
Proc. Natl. Acad. Sci. Usa V. 103 305 2006
PubMed-ID: 16384918 | Reference-DOI: 10.1073/PNAS.0507109103

Molecule 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PREP4
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 27-200
	Gene	:	SDBA
	Organism Scientific	:	CLOSTRIDIUM THERMOCELLUM
	Organism Taxid	:	203119
	Strain	:	ATCC 27405
	Synonym	:	TYPE II COHESIN

Molecule 2 - CELLULOSOMAL SCAFFOLDING PROTEIN A
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1691-1853
	Gene	:	CIPA
	Organism Scientific	:	CLOSTRIDIUM THERMOCELLUM
	Organism Taxid	:	1515
	Synonym	:	TYPE II DOCKERIN-X, CELLULOSOMAL GLYCOPROTEIN S1/SL, CELLULOSE INTEGRATING PROTEIN A, COHESIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:135 , ASN B:137 , ASN B:139 , ALA B:141 , ASP B:146	BINDING SITE FOR RESIDUE CA B 501
2	AC2	SOFTWARE	ASP B:102 , VAL B:104 , ASP B:106 , SER B:108 , ASP B:113 , HOH B:503	BINDING SITE FOR RESIDUE CA B 502

(no "SS Bond" information available for 2B59)

(no "Cis Peptide Bond" information available for 2B59)

(no "SAP(SNP)/Variant" information available for 2B59)

Asymmetric/Biological Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DOCKERIN	PS51766	Dockerin domain profile.	CIPB_CLOTM	704-771	1	B:96-163
1	DOCKERIN	PS51766	Dockerin domain profile.	CIPA_CLOTH	1785-1852	1	B:96-163
2	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	CIPB_CLOTM	710-729 743-762	2	B:102-121 B:135-154
2	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	CIPA_CLOTH	1791-1810 1824-1843	2	B:102-121 B:135-154
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CIPB_CLOTM	743-755	1	B:135-147
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CIPA_CLOTH	1824-1836	1	B:135-147

(no "Exon" information available for 2B59)

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:166
 aligned with A3DF10_CLOTH | A3DF10 from UniProtKB/TrEMBL  Length:631

    Alignment length:166
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
        A3DF10_CLOTH     30 KASSIELKFDRNKGEVGDILIGTVRINNIKNFAGFQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEKGILNFALAYSYIAGYKETGVAEESGIIAKIGFKILQKKSTAVKFQDTLSMPGAISGTQLFDWDGEVITGYEVIQPDVLSL  195
               SCOP domains d2b59a1 A:17-182 Scaffolding dockerin binding protein A, SdbA                                                                                                          SCOP domains
               CATH domains 2b59A00 A:17-182  [code=2.60.40.680, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeeee....eeeeeeeee.....eeee.....................hhhh.eeeee..hhhh.eeeeeeee.hhhhhhhh......eeeeeeeeee........ee............eeeee....ee...eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b59 A   17 KASSIELKFDRNKGEVGDILIGTVRINNIKNFAGFQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEKGILNFALAYSYIAGYKETGVAEESGIIAKIGFKILQKKSTAVKFQDTLSMPGAISGTQLFDWDGEVITGYEVIQPDVLSL  182
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain A from PDB  Type:PROTEIN  Length:166
 aligned with P71143_CLOTM | P71143 from UniProtKB/TrEMBL  Length:631

    Alignment length:166
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
        P71143_CLOTM     30 KASSIELKFDRNKGEVGDILIGTVRINNIKNFAGFQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEKGILNFALAYSYIAGYKETGVAEESGIIAKIGFKILQKKSTAVKFQDTLSMPGAISGTQLFDWDGEVITGYEVIQPDVLSL  195
               SCOP domains d2b59a1 A:17-182 Scaffolding dockerin binding protein A, SdbA                                                                                                          SCOP domains
               CATH domains 2b59A00 A:17-182  [code=2.60.40.680, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeeee....eeeeeeeee.....eeee.....................hhhh.eeeee..hhhh.eeeeeeee.hhhhhhhh......eeeeeeeeee........ee............eeeee....ee...eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b59 A   17 KASSIELKFDRNKGEVGDILIGTVRINNIKNFAGFQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEKGILNFALAYSYIAGYKETGVAEESGIIAKIGFKILQKKSTAVKFQDTLSMPGAISGTQLFDWDGEVITGYEVIQPDVLSL  182
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:156
                                  1706      1716      1726      1736      1746      1756      1766      1776      1786      1796      1806      1816      1826      1836      1846      
          CIPA_CLOTH   1697 GYKVSGYILPDFSFDATVAPLVKAGFKVEIVGTELYAVTDANGYFEITGVPANASGYTLKISRATYLDRVIANVVVTGDTSVSTSQAPIMMWVGDIVKDNSINLLDVAEVIRCFNATKGSANYVEELDINRNGAINMQDIMIVHKHFGATSSDYDA 1852
               SCOP domains d2b59b2 B:8-103 Cellulosomal scaffolding protein A                                              d2b59b1 B:104-163 Cellulosomal scaffolding protein A         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.......hhhhhhh..eeee.....eee.....eeeeeee..eeeeeeeeee..ee..eeeeeeee...ee.......eee.eee.......hhhhhhhhhhh..........hhhhh.......hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------DOCKERIN  PDB: B:96-163 UniProt: 1785-1852                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------CLOS_CELLULOSOME_RPT-------------CLOS_CELLULOSOME_RPT--------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    ---------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2b59 B    8 GYKVSGYILPDFSFDATVAPLVKAGFKVEIVGTELYAVTDANGYFEITGVPANASGYTLKISRATYLDRVIANVVVTGDTSVSTSQAPIMMWVGDIVKDNSINLLDVAEVIRCFNATKGSANYVEELDINRNGAINMQDIMIVHKHFGATSSDYDA  163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with CIPB_CLOTM | Q01866 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:156
                                   625       635       645       655       665       675       685       695       705       715       725       735       745       755       765      
          CIPB_CLOTM    616 GYKVSGYILPDFSFDATVAPLVKAGFKVEIVGTELYAVTDANGYFEITGVPANASGYTLKISRATYLDRVIANVVVTGDTSVSTSQAPIMMWVGDIVKDNSINLLDVAEVIRCFNATKGSANYVEELDINRNGAINMQDIMIVHKHFGATSSDYDA  771
               SCOP domains d2b59b2 B:8-103 Cellulosomal scaffolding protein A                                              d2b59b1 B:104-163 Cellulosomal scaffolding protein A         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.......hhhhhhh..eeee.....eee.....eeeeeee..eeeeeeeeee..ee..eeeeeeee...ee.......eee.eee.......hhhhhhhhhhh..........hhhhh.......hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------DOCKERIN  PDB: B:96-163 UniProt: 704-771                             PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------CLOS_CELLULOSOME_RPT-------------CLOS_CELLULOSOME_RPT--------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    ---------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2b59 B    8 GYKVSGYILPDFSFDATVAPLVKAGFKVEIVGTELYAVTDANGYFEITGVPANASGYTLKISRATYLDRVIANVVVTGDTSVSTSQAPIMMWVGDIVKDNSINLLDVAEVIRCFNATKGSANYVEELDINRNGAINMQDIMIVHKHFGATSSDYDA  163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.680, no name defined] (14)

Clostridium thermocellum atcc 27405. Organism_taxid: 203119. Strain: atcc 27405. (1)

2b59A00

A:17-182

(no "Pfam Domain" information available for 2B59)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (P71143_CLOTM | P71143)

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.
biological process
	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.

Chain A (A3DF10_CLOTH | A3DF10)

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.
biological process
	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.

Chain B (CIPA_CLOTH | Q06851)

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:0030248	cellulose binding	Interacting selectively and non-covalently with cellulose.
	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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	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: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 B (CIPB_CLOTM | Q01866)

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:0030248	cellulose binding	Interacting selectively and non-covalently with cellulose.
	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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	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: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/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 2B59)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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