3VO0 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BETA-GLUCURONIDASE FROM ACIDOBACTERIUM CAPSULATUM COVALENT-BONDED WITH 2-DEOXY-2-FLUORO-D-GLUCURONIC ACID

Authors :   M. Momma, Z. Fujimoto, M. Michikawa, H. Ichinose, S. Jongkees, M. Yoshi Y. Kotake, P. Biely, Y. Tsumuraya, S. Withers, S. Kaneko

Date :   18 Jan 12 (Deposition) - 22 Feb 12 (Release) - 19 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (4x)

Keywords :   Tim Barrel, Greek-Key, Glycoside Hydrolase Family 79, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Michikawa, H. Ichinose, M. Momma, P. Biely, S. Jongkees, M. Yoshida T. Kotake, Y. Tsumuraya, S. G. Withers, Z. Fujimoto, S. Kaneko
Structural And Biochemical Characterization Of Glycoside Hydrolase Family 79 Beta-Glucuronidase From Acidobacterium Capsulatum
J. Biol. Chem. V. 287 14069 2012
PubMed-ID: 22367201 | Reference-DOI: 10.1074/JBC.M112.346288

Molecule 1 - BETA-GLUCURONIDASE
	Chains	:	A
	EC Number	:	3.2.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ACP_2665
	Organism Scientific	:	ACIDOBACTERIUM CAPSULATUM
	Organism Taxid	:	240015
	Strain	:	ATCC 51196

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	DNF	3	Ligand/Ion	2,4-DINITROPHENOL
2	GUF	2	Ligand/Ion	2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANURONIC ACID
3	GUZ	1	Ligand/Ion	2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANURONIC ACID
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	DNF	3	Ligand/Ion	2,4-DINITROPHENOL
2	GUF	2	Ligand/Ion	2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANURONIC ACID
3	GUZ	1	Ligand/Ion	2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANURONIC ACID
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (4, 16)

No.	Name	Count	Type	Full Name
1	DNF	6	Ligand/Ion	2,4-DINITROPHENOL
2	GUF	4	Ligand/Ion	2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANURONIC ACID
3	GUZ	2	Ligand/Ion	2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANURONIC ACID
4	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (4, 32)

No.	Name	Count	Type	Full Name
1	DNF	12	Ligand/Ion	2,4-DINITROPHENOL
2	GUF	8	Ligand/Ion	2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANURONIC ACID
3	GUZ	4	Ligand/Ion	2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANURONIC ACID
4	PO4	8	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:45 , GLY A:79 , ASN A:80 , PRO A:104 , ASP A:105 , ASN A:172 , GLU A:173 , TYR A:243 , GLU A:287 , TYR A:292 , GLN A:293 , GLY A:294 , HIS A:327 , TYR A:334 , HOH A:886	BINDING SITE FOR RESIDUE GUZ A 501
2	AC2	SOFTWARE	HIS A:109 , ALA A:110 , ASN A:180 , DNF A:503	BINDING SITE FOR RESIDUE GUF A 502
3	AC3	SOFTWARE	ASN A:80 , GLU A:83 , TYR A:84 , GLY A:107 , HIS A:108 , HIS A:109 , ALA A:110 , ASN A:180 , ILE A:182 , GUF A:502 , HOH A:854 , HOH A:857	BINDING SITE FOR RESIDUE DNF A 503
4	AC4	SOFTWARE	PHE A:86 , ARG A:113 , LYS A:143 , THR A:145 , PRO A:414 , SER A:415 , TYR A:452 , ALA A:480 , DNF A:505 , DNF A:506 , HOH A:795	BINDING SITE FOR RESIDUE GUF A 504
5	AC5	SOFTWARE	PHE A:86 , TRP A:87 , ASN A:88 , GLY A:144 , THR A:145 , ASN A:148 , TYR A:452 , GUF A:504 , DNF A:506 , HOH A:783	BINDING SITE FOR RESIDUE DNF A 505
6	AC6	SOFTWARE	ASN A:88 , SER A:415 , GLY A:416 , THR A:417 , GLN A:450 , GLU A:451 , TYR A:452 , GUF A:504 , DNF A:505 , HOH A:739 , HOH A:919	BINDING SITE FOR RESIDUE DNF A 506
7	AC7	SOFTWARE	GLY A:103 , GLY A:330 , TYR A:331 , GLY A:332 , HOH A:778 , HOH A:792 , HOH A:875	BINDING SITE FOR RESIDUE PO4 A 507
8	AC8	SOFTWARE	LYS A:92 , ARG A:420 , GLU A:422 , HIS A:463 , ARG A:465	BINDING SITE FOR RESIDUE PO4 A 508

(no "SS Bond" information available for 3VO0)

Asymmetric Unit

No.	Residues
1	Gly A:214	-	Pro A:215
2	Gly A:246	-	Pro A:247

(no "SAP(SNP)/Variant" information available for 3VO0)

(no "PROSITE Motif" information available for 3VO0)

(no "Exon" information available for 3VO0)

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:466
 aligned with C1F2K5_ACIC5 | C1F2K5 from UniProtKB/TrEMBL  Length:475

    Alignment length:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   475        
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       | -      
         C1F2K5_ACIC5    18 SPVRVGLSVDASALGHTIPPDYTGLSYEQAQMANPNYFSGANTQLAGFLRTLGRQGVLRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWKLIYGLNLGKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYRNGIRPASYDFAAYAGDWQRFFTAIRKRVPNAPFAGPDTAYNTKWLVPFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPFRLTETNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFHGGGYGWYTPVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIALFNKNLDADVEVAISGVASPSGTVLRLEAPRADDTTDVTFGGAPVGASGSWSPLVQEYVPGHSGQFVLHMRKASGALLEFA--------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeee.....eeeee.hhhhh.......hhhhhhhhhhhh...eeeeehhhhh.eee....hhhhh.................eeehhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.....eeeeeeeee........hhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhh...eeeee........eeee...eeeehhhhhhhhhhhhhh.eeeeeeeee.......eeeeeeee....eeeeeee......eeeeee.....eeeeeeee..........ee.....hhhhh......eeee.....eeeee...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vo0 A  18 SPVRVGLSVDASALGHTIPPDYTGLSYEQAQMANPNYFSGANTQLAGFLRTLGRQGVLRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWKLIYGLNLGKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYRNGIRPASYDFAAYAGDWQRFFTAIRKRVPNAPFAGPDTAYNTKWLVPFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPFRLTETNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFHGGGYGWYTPVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIALFNKNLDADVEVAISGVASPSGTVLRLEAPRADDTTDVTFGGAPVGASGSWSPLVQEYVPGHSGQFVLHMRKASGALLEFAKLAAALQH 483
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477

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 3VO0)

(no "CATH Domain" information available for 3VO0)

(no "Pfam Domain" information available for 3VO0)

Asymmetric Unit(hide GO term definitions)

Chain A (C1F2K5_ACIC5 | C1F2K5)

molecular function
	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.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		DNF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GUF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GUZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:214 - Pro A:215	[ RasMol ]
		Gly A:246 - Pro A:247	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	3vo0
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	3.2.1.31
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	C1F2K5_ACIC5 \| C1F2K5	:	5g0m 5g0q 5l77
UniProtKB/TrEMBL
	C1F2K5_ACIC5 \| C1F2K5	:	3vny 3vnz

3vny	THE SAME PROTEIN WITHOUT LIGAND
3vnz	THE SAME PROTEIN COMPLEXED WITH GLUCURONIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (3, 3)

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