2VN5 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   THE CLOSTRIDIUM CELLULOLYTICUM DOCKERIN DISPLAYS A DUAL BINDING MODE FOR ITS COHESIN PARTNER

Authors :   B. A. Pinheiro, J. A. M. Prates, M. R. Proctor, H. J. Gilbert, G. J. Davies V. A. Money, C. Martinez-Fleites, E. A. Bayer, C. M. G. A. Fontes, H. P. F

Date :   31 Jan 08 (Deposition) - 20 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Carbohydrate Metabolism, Polysaccharide Degradation, Cohesin, Dockerin, Hydrolase, Cellulosome, Glycosidase, Cellulose Degradation, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Pinheiro, M. R. Proctor, C. Martinez-Fleites, J. A. M. Prates, V. A. Money, G. J. Davies, E. A. Bayer, C. M. G. A. Fontes, H. P. Fierobe, H. J. Gilbert
The Clostridium Cellulolyticum Dockerin Displays A Dual Binding Mode For Its Cohesin Partner.
J. Biol. Chem. V. 283 18422 2008
PubMed-ID: 18445585 | Reference-DOI: 10.1074/JBC.M801533200

Molecule 1 - SCAFFOLDING PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 277-427
	Organism Scientific	:	CLOSTRIDIUM CELLULOLYTICUM
	Organism Taxid	:	1521
	Synonym	:	COHESIN

Molecule 2 - ENDOGLUCANASE A
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 410-475
	Organism Scientific	:	CLOSTRIDIUM CELLULOLYTICUM
	Organism Taxid	:	1521
	Synonym	:	DOCKERIN, ENDO-1,4-BETA-GLUCANASE A, EGCCA, CELLULASE A

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:38 , ASN B:40 , ASP B:42 , GLU B:44 , ASP B:49 , HOH B:1027	BINDING SITE FOR RESIDUE CA B 101
2	AC2	SOFTWARE	ASP B:7 , ASN B:9 , ASP B:11 , ASN B:13 , ASP B:18 , HOH B:1012	BINDING SITE FOR RESIDUE CA B 102
3	AC3	SOFTWARE	ASP D:38 , ASN D:40 , ASP D:42 , GLU D:44 , ASP D:49 , HOH D:1025	BINDING SITE FOR RESIDUE CA D 101
4	AC4	SOFTWARE	ASP D:7 , ASN D:9 , ASP D:11 , ASN D:13 , ASP D:18 , HOH D:1010	BINDING SITE FOR RESIDUE CA D 102

(no "SS Bond" information available for 2VN5)

(no "Cis Peptide Bond" information available for 2VN5)

(no "SAP(SNP)/Variant" information available for 2VN5)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	GUNA_CLOCE	415-434 446-465	4	B:7-26 D:7-26 B:38-57 D:38-57
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	GUNA_CLOCE	415-427	2	B:7-19 D:7-19

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	GUNA_CLOCE	415-434 446-465	2	B:7-26 - B:38-57 -
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	GUNA_CLOCE	415-427	1	B:7-19 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CLOS_CELLULOSOME_RPT	PS00448	Clostridium cellulosome enzymes repeated domain signature.	GUNA_CLOCE	415-434 446-465	2	- D:7-26 - D:38-57
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	GUNA_CLOCE	415-427	1	- D:7-19

(no "Exon" information available for 2VN5)

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:142
 aligned with Q45996_9FIRM | Q45996 from UniProtKB/TrEMBL  Length:1546

    Alignment length:142
                                   295       305       315       325       335       345       355       365       375       385       395       405       415       425  
         Q45996_9FIRM   286 DSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP 427
               SCOP domains d2vn5a_ A: Cohesin domain                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.eeee....eeeeeeeee.hhhhh.eeeeeeeee.....eeeeeeee.....hhhhheeeeee..eeeeeee............eeeeeeeeee......eeeeeee....eeee........eeee.eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn5 A  11 DSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP 152
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with GUNA_CLOCE | P17901 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:59
                                   420       430       440       450       460         
           GUNA_CLOCE   411 IVYGDYNNDGNVDALDFAGLKKYIMAADHAYVKNLDVNLDNEVNAFDLAILKKYLLGMV 469
               SCOP domains d2vn5b_ B: automated match   es                             SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhh---..hhhhh.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----EF_HAND_1    ------------------CLOS_CELLULOSOME_RPT---- PROSITE (1)
                PROSITE (2) ----CLOS_CELLULOSOME_RPT----------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------- Transcript
                 2vn5 B   3 IVYGDYNNDGNVDALDFAGLKKYIMA---AYVKNLDVNLDNEVNSTDLAILKKYLLGMV  61
                                    12        22     |  32        42        52         
                                                    28  32

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with Q45996_9FIRM | Q45996 from UniProtKB/TrEMBL  Length:1546

    Alignment length:151
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426 
         Q45996_9FIRM   277 TVLPKDIPGDSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP 427
               SCOP domains d2vn5c   _ C: Cohesin domain                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......---..eeeee.eeee....eeeeeeeee.hhhhh...eeeeeee.....eeeeeeee.....hhhhheeeeee..eeeeeee............eeeeeeeeee......eeeeeeee....ee.........eeee.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn5 C   2 TVLPKD---DSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP 152
                                 |  11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
                                 7  11

Chain D from PDB  Type:PROTEIN  Length:55
 aligned with GUNA_CLOCE | P17901 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:58
                                   420       430       440       450       460        
           GUNA_CLOCE   411 IVYGDYNNDGNVDALDFAGLKKYIMAADHAYVKNLDVNLDNEVNAFDLAILKKYLLGM 468
               SCOP domains d2vn5d_ D: automated match   es                            SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------Dockerin_1-2vn5D01   -- Pfam domains (1)
           Pfam domains (2) -----------------------------------Dockerin_1-2vn5D02   -- Pfam domains (2)
           Pfam domains (3) -----------------------------------Dockerin_1-2vn5D03   -- Pfam domains (3)
           Pfam domains (4) -----------------------------------Dockerin_1-2vn5D04   -- Pfam domains (4)
         Sec.struct. author ............hhhhhhhhhhhhhh---..hhhhh.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----EF_HAND_1    ------------------CLOS_CELLULOSOME_RPT--- PROSITE (1)
                PROSITE (2) ----CLOS_CELLULOSOME_RPT---------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                 2vn5 D   3 IVYGDYNNDGNVDALDFAGLKKYIMA---AYVKNLDVNLDNEVNSTDLAILKKYLLGM  60
                                    12        22     |  32        42        52        
                                                    28  32

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 "CATH Domain" information available for 2VN5)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: Dockerin_1 (3)

Clostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10) (2)

1a	Dockerin_1-2vn5D01	D:38-58
1b	Dockerin_1-2vn5D02	D:38-58
1c	Dockerin_1-2vn5D03	D:38-58
1d	Dockerin_1-2vn5D04	D:38-58

Asymmetric Unit(hide GO term definitions)

Chain A,C (Q45996_9FIRM | Q45996)

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: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: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,D (GUNA_CLOCE | P17901)

molecular function
	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.
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.

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	2vn5
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	Q45996_9FIRM \| Q45996
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UniProtKB/Swiss-Prot
	GUNA_CLOCE \| P17901	:	1edg 2vn6
UniProtKB/TrEMBL
	Q45996_9FIRM \| Q45996	:	1ehx 1g1k 1g43 2vn6

1edg	SINGLE CRYSTAL STRUCTURE DETERMINATION OF THE CATALYTIC DOMAIN OF CELCCA CARRIED OUT AT 15 DEGREE C
1ehx	NMR SOLUTION STRUCTURE OF THE LAST UNKNOWN MODULE OF THECELLULOSOMAL SCAFFOLDIN PROTEIN CIPC OF CLOSTRIDUMCELLULOLYTICUM
1g1k	COHESIN MODULE FROM THE CELLULOSOME OF CLOSTRIDIUMCELLULOLYTICUM
1g43	CRYSTAL STRUCTURE OF A FAMILY IIIA CBD FROM CLOSTRIDIUMCELLULOLYTICUM
2vn6	THE CLOSTRIDIUM CELLULOLYTICUM DOCKERIN DISPLAYS A DUAL BINDING MODE FOR ITS COHESIN PARTNER

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (2, 6)

Exons (0, 0)

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SCOP Domains (2, 4)

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Gene Ontology (11, 13)

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