3K4D - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI BETA-GLUCURONIDASE WITH THE GLUCARO-D-LACTAM INHIBITOR BOUND

Authors :   B. D. Wallace, M. R. Redinbo

Date :   05 Oct 09 (Deposition) - 17 Nov 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

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

Keywords :   Alpha/Beta Barrel, Sugar-Binding Domain, Beta-Sandwich Domain, Glycosyl Hydrolase, Glucaro-D-Lactam, Glycosidase, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Wallace, H. Wang, K. T. Lane, J. E. Scott, J. Orans, J. S. Koo, M. Venkatesh, C. Jobin, L. A. Yeh, S. Mani, M. R. Redinbo
Alleviating Cancer Drug Toxicity By Inhibiting A Bacterial Enzyme.
Science V. 330 831 2010
PubMed-ID: 21051639 | Reference-DOI: 10.1126/SCIENCE.1191175

Molecule 1 - BETA-GLUCURONIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B1617, GURA, GUSA, JW1609, UIDA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	GUS, BETA-D-GLUCURONOSIDE GLUCURONOSOHYDROLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	EVA	2	Ligand/Ion	(2S,3R,4S,5R)-3,4,5-TRIHYDROXY-6-OXOPIPERIDINE-2-CARBOXYLIC ACID

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	EVA	4	Ligand/Ion	(2S,3R,4S,5R)-3,4,5-TRIHYDROXY-6-OXOPIPERIDINE-2-CARBOXYLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:163 , HIS A:330 , ASN A:412 , GLU A:413 , ASN A:466 , TYR A:468 , TYR A:472 , GLU A:504 , TRP A:549 , ARG A:562 , ASN A:566 , LYS A:568 , HOH A:630 , HOH A:647	BINDING SITE FOR RESIDUE EVA A 604
2	AC2	SOFTWARE	ASP B:163 , HIS B:330 , ASN B:412 , GLU B:413 , ASN B:466 , TYR B:468 , TYR B:472 , GLU B:504 , TRP B:549 , ARG B:562 , ASN B:566 , LYS B:568	BINDING SITE FOR RESIDUE EVA B 604

(no "SS Bond" information available for 3K4D)

Asymmetric Unit

No.	Residues
1	Ile B:143	-	Pro B:144

(no "SAP(SNP)/Variant" information available for 3K4D)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F2_1	PS00719	Glycosyl hydrolases family 2 signature 1.	BGLR_ECOLI	324-349	2	A:324-349 B:324-349
2	GLYCOSYL_HYDROL_F2_2	PS00608	Glycosyl hydrolases family 2 acid/base catalyst.	BGLR_ECOLI	399-413	2	A:399-413 B:399-413

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F2_1	PS00719	Glycosyl hydrolases family 2 signature 1.	BGLR_ECOLI	324-349	4	A:324-349 B:324-349
2	GLYCOSYL_HYDROL_F2_2	PS00608	Glycosyl hydrolases family 2 acid/base catalyst.	BGLR_ECOLI	399-413	4	A:399-413 B:399-413

(no "Exon" information available for 3K4D)

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:596
 aligned with BGLR_ECOLI | P05804 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:603
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598   
           BGLR_ECOLI     - --MLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMVITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVVIDETAAVGFNLSLGIGFEAGNKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGG 601
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee......eeeeee........hhhhh.....eee...........hhhhhh...eeeeeeeee.hhhhh..eeeeee.....eeeeee...eeeeee.....eeee.hhhh....eeeeeeeee..........eeeee.....eeeee.............eeeeee...eeeeeeeee.......eeeeeeeeee..eeeeeee.....eeeeee...eeeeee............eeeeeeee....eeeeeeee....eeee..eeee..ee..eeeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh.eeeee...........-------...........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh....eeee...........hhhhh..eeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhhhhh..eeeeeee............................hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F2_1      -------------------------------------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4d A  -1 SHMLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMVITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVVIDETAAVGFNLSLG-------KPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGG 601
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   |     - |     378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598   
                                                                                                                                                                                                                                                                                                                                                                                                     362     370

Chain B from PDB  Type:PROTEIN  Length:596
 aligned with BGLR_ECOLI | P05804 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:603
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598   
           BGLR_ECOLI     - --MLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMVITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVVIDETAAVGFNLSLGIGFEAGNKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGG 601
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Glyco_hydro_2_N-3k4dB01 B:9-180                                                                                                                                             -Glyco_hydro_2-3k4dB05 B:182-272                                                            -Glyco_hydro_2_C-3k4dB03 B:274-593                                                                                                                                                                                                                                                                                               -------- Pfam domains (1)
           Pfam domains (2) ----------Glyco_hydro_2_N-3k4dB02 B:9-180                                                                                                                                             -Glyco_hydro_2-3k4dB06 B:182-272                                                            -Glyco_hydro_2_C-3k4dB04 B:274-593                                                                                                                                                                                                                                                                                               -------- Pfam domains (2)
         Sec.struct. author ............eee....eeeeee.........hhhhh.....eeee..........hhhhhh...eeeeeeeee........eeeeee.....eeeeee...eeeeee.....eeee.hhhh....eeeeeeeee..........eeeee.....eeeee.............eeeeee...eeeeeeeee.......eeeeeeeeee.......ee.....eee..........ee............eeeeeeee....eeeeeeee....eeee..eeee..eee...eeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh.eeeee...........-------...........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeee.................eeee..........hhhhhhhhhhhhhhhhhhhh...eeeeee................hhhhhhhhhhhhhhhhhhh..eeeeee..............................hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F2_1      -------------------------------------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4d B  -1 SHMLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMVITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVVIDETAAVGFNLSLG-------KPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGG 601
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   |     - |     378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598   
                                                                                                                                                                                                                                                                                                                                                                                                     362     370

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 3K4D)

(no "CATH Domain" information available for 3K4D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BGLR_ECOLI | P05804)

molecular function
	GO:0004566	beta-glucuronidase activity	Catalysis of the reaction: a beta-D-glucuronoside + H2O = an alcohol + D-glucuronate.
	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:0019391	glucuronoside catabolic process	The chemical reactions and pathways resulting in the breakdown of glucuronosides, compound composed of a hydroxy compound linked to a glucuronate residue.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

Asymmetric Unit
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	Cis Peptide Bonds
		Ile B:143 - Pro B:144	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3k4d
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	BGLR_ECOLI \| P05804
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	3.2.1.31
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	BGLR_ECOLI \| P05804
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UniProtKB/Swiss-Prot
	BGLR_ECOLI \| P05804	:	3k46 3k4a 3lpf 3lpg 4jhz 5czk

3k46	CRYSTAL STRUCTURE OF NATIVE, UNBOUND, E. COLI BETA- GLUCURONIDASE
3k4a	CRYSTAL STRUCTURE OF SELENOMETHIONINE SUBSTITUTED E. COLI BETA-GLUCURONIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (3, 6)

Gene Ontology (9, 9)

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