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Title :   CRYSTAL STRUCTURE OF 6-PHOSPHO-BETA-GLUCOSIDASE FROM LACTOBACILLUS PLANTARUM

Authors :   K. Michalska, C. Hatzos-Skintges, J. Bearden, M. Kohler, A. Joachimia Center For Structural Genomics (Mcsg)

Date :   10 Feb 11 (Deposition) - 09 Mar 11 (Release) - 02 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Michalska, K. Tan, H. Li, C. Hatzos-Skintges, J. Bearden, G. Babnigg, A. Joachimiak
Gh1-Family 6-P-Beta-Glucosidases From Human Microbiome Lactic Acid Bacteria.
Acta Crystallogr. , Sect. D V. 69 451 2013
PubMed-ID: 23519420 | Reference-DOI: 10.1107/S0907444912049608

Molecule 1 - 6-PHOSPHO-BETA-GLUCOSIDASE
	Chains	:	A
	EC Number	:	3.2.1.86
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG9
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PBG1, LP_0440
	Organism Scientific	:	LACTOBACILLUS PLANTARUM
	Organism Taxid	:	1590
	Strain	:	WCFS1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
3	MSE	13	Mod. Amino Acid	SELENOMETHIONINE
4	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 38)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
3	MSE	26	Mod. Amino Acid	SELENOMETHIONINE
4	PO4	8	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:180 , ASN A:183 , ALA A:243 , ARG A:267 , PO4 A:480 , HOH A:525 , HOH A:679 , HOH A:733 , HOH A:757 , HOH A:774 , HOH A:808 , HOH A:917	BINDING SITE FOR RESIDUE BGC A 479
2	AC2	SOFTWARE	TRP A:349 , ALA A:430 , ALA A:431 , SER A:432 , LYS A:438 , TYR A:440 , BGC A:479 , HOH A:610 , HOH A:718 , HOH A:743 , HOH A:808	BINDING SITE FOR RESIDUE PO4 A 480
3	AC3	SOFTWARE	HIS A:201 , PRO A:203 , GLY A:204 , ARG A:207 , HOH A:852	BINDING SITE FOR RESIDUE PO4 A 481
4	AC4	SOFTWARE	TYR A:27 , VAL A:55 , HIS A:64 , GLN A:65 , HOH A:535 , HOH A:666	BINDING SITE FOR RESIDUE PO4 A 482
5	AC5	SOFTWARE	HIS A:334 , LYS A:343	BINDING SITE FOR RESIDUE PO4 A 483
6	AC6	SOFTWARE	TRP A:362 , HOH A:628 , HOH A:668 , HOH A:765 , HOH A:801	BINDING SITE FOR RESIDUE ACT A 484

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

(no "Cis Peptide Bond" information available for 3QOM)

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

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

(no "Exon" information available for 3QOM)

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)
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Chain A from PDB  Type:PROTEIN  Length:479
 aligned with F9UU25_LACPL | F9UU25 from UniProtKB/TrEMBL  Length:478

    Alignment length:479
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469         
         F9UU25_LACPL     - -MTIKGRAFPEGFLWGGAVAAHQLEGGYKEGGKGLSTADIMTLGTNERPREITDGVVAGKYYPNHQAIDFYHRYPEDIELFAEMGFKCFRTSIAWTRIFPNGDESEPNEAGLQFYDDLFDECLKNGIQPVVTLAHFEMPYHLVKQYGGWRNRKLIQFYLNFAKVCFERYRDKVTYWMTFNEINNQTNFESDGAMLTDSGIIHQPGENRERWMYQAAHYELVASAAAVQLGHQINPDFQIGCMIAMCPIYPLTAAPADVLFAQRAMQTRFYFADVHCNGTYPQWLRNRFESEHFNLDITAEDLKILQAGTVDYIGFSYYMSFTVKDTGKLAYNEEHDLVKNPYVKASDWGWQVDPVGLRYAMNWFTDRYHLPLFIVENGLGAIDKKTADNQIHDDYRIDYLTDHLRQIKLAVLEDGVDLIGYTPWGCIDLVAASTGQMSKRYGFIYVDENDDGSGSLKRYKKDSFTWFQHVIATNGAEIE 478
               SCOP domains d3qoma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhhhhh...hhhhh..hhhhhh...........................hhhhhhhhhhhhhhhhh..eeeee.hhhhhh........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...eee...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhh...eeeeee...eee.............ee...............hhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhhhhh....eeee......................eee...........eeehhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qom A   0 AmTIKGRAFPEGFLWGGAVAAHQLEGGYKEGGKGLSTADImTLGTNERPREITDGVVAGKYYPNHQAIDFYHRYPEDIELFAEmGFKCFRTSIAWTRIFPNGDESEPNEAGLQFYDDLFDECLKNGIQPVVTLAHFEmPYHLVKQYGGWRNRKLIQFYLNFAKVCFERYRDKVTYWmTFNEINNQTNFESDGAmLTDSGIIHQPGENRERWmYQAAHYELVASAAAVQLGHQINPDFQIGCmIAmCPIYPLTAAPADVLFAQRAmQTRFYFADVHCNGTYPQWLRNRFESEHFNLDITAEDLKILQAGTVDYIGFSYYmSFTVKDTGKLAYNEEHDLVKNPYVKASDWGWQVDPVGLRYAmNWFTDRYHLPLFIVENGLGAIDKKTADNQIHDDYRIDYLTDHLRQIKLAVLEDGVDLIGYTPWGCIDLVAASTGQmSKRYGFIYVDENDDGSGSLKRYKKDSFTWFQHVIATNGAEIE 478
                             |       9        19        29        39|       49        59        69        79   |    89        99       109       119       129       139       149       159       169      |179       189   |   199       209 |     219       229       239 |  |  249       259    |  269       279       289       299       309       319       329       339       349       359|      369       379       389       399       409       419       429      |439       449       459       469         
                             |                                     40-MSE                                     83-MSE                                               137-MSE                                176-MSE          193-MSE           211-MSE                       241-MSE                264-MSE                                               318-MSE                                   360-MSE                                                                     436-MSE                                      
                             1-MSE                                                                                                                                                                                                                                            244-MSE

Legend:		→ Mismatch	(orange background)
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	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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: automated matches (180)

Protein domain: automated matches (180)

Lactobacillus plantarum [TaxId: 1590] (2)

d3qoma_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (F9UU25_LACPL | F9UU25)

molecular function
	GO:0008706	6-phospho-beta-glucosidase activity	Catalysis of the reaction: 6-phospho-beta-D-glucoside-(1,4)-D-glucose + H2O = D-glucose 6-phosphate + glucose.
	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: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.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Unit
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Description

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Ligands, Modified Residues, Ions (4, 19)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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