3PN8 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF 6-PHOSPHO-BETA-GLUCOSIDASE FROM STREPTOCOCCUS MUTANS UA159

Authors :   K. Tan, H. Li, J. Bearden, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)

Date :   18 Nov 10 (Deposition) - 15 Dec 10 (Release) - 08 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.69

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

Keywords :   Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, (Beta/Alpha)8 Barrel, Beta-Glucosidase, Cytoplasmic, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, H. Li, J. Bearden, A. Joachimiak
The Crystal Structure Of 6-Phospho-Beta-Glucosidase From Streptococcus Mutants Ua159
To Be Published
PubMed: search

Molecule 1 - PUTATIVE PHOSPHO-BETA-GLUCOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.86
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	BGL, SMU_1601, STREPTOCOCCUS MUTANS
	Organism Scientific	:	STREPTOCOCCUS MUTANS
	Organism Taxid	:	1309
	Strain	:	UA159
	Synonym	:	6-PHOSPHO-BETA-GLUCOSIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 62)

No.	Name	Count	Type	Full Name
1	FMT	10	Ligand/Ion	FORMIC ACID
2	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 35)

No.	Name	Count	Type	Full Name
1	FMT	7	Ligand/Ion	FORMIC ACID
2	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 27)

No.	Name	Count	Type	Full Name
1	FMT	3	Ligand/Ion	FORMIC ACID
2	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 62)

No.	Name	Count	Type	Full Name
1	FMT	10	Ligand/Ion	FORMIC ACID
2	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (32, 32)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:349 , SER A:430 , ALA A:431 , GLY A:432 , LYS A:438 , TYR A:440 , HOH A:620 , HOH A:654 , HOH A:689	BINDING SITE FOR RESIDUE SO4 A 478
02	AC2	SOFTWARE	ARG A:437	BINDING SITE FOR RESIDUE SO4 A 479
03	AC3	SOFTWARE	PHE A:292 , THR A:293 , GLU A:294 , LYS A:297	BINDING SITE FOR RESIDUE SO4 A 480
04	AC4	SOFTWARE	ASN A:249 , LYS A:251 , HOH A:617	BINDING SITE FOR RESIDUE SO4 A 481
05	AC5	SOFTWARE	LYS A:251 , TYR A:328 , HOH A:748 , HOH A:772 , HOH B:676	BINDING SITE FOR RESIDUE SO4 A 482
06	AC6	SOFTWARE	ARG A:147 , ASP A:151 , ARG A:220 , ARG A:295 , HOH A:758	BINDING SITE FOR RESIDUE SO4 A 483
07	AC7	SOFTWARE	ARG A:162 , LYS A:165	BINDING SITE FOR RESIDUE SO4 A 484
08	AC8	SOFTWARE	ASN A:7 , LEU A:417 , MSE A:418 , HOH A:537	BINDING SITE FOR RESIDUE PEG A 485
09	AC9	SOFTWARE	THR A:247 , VAL A:337 , LYS A:338 , HOH A:594	BINDING SITE FOR RESIDUE PEG A 486
10	BC1	SOFTWARE	MSE A:314 , HOH A:515	BINDING SITE FOR RESIDUE PEG A 487
11	BC2	SOFTWARE	LYS A:281 , ARG A:285 , TYR A:327 , ASP B:411	BINDING SITE FOR RESIDUE PEG A 488
12	BC3	SOFTWARE	PRO A:102 , ASN A:103 , GLU A:104 , ALA A:105 , HOH A:500	BINDING SITE FOR RESIDUE PEG A 489
13	BC4	SOFTWARE	LYS A:338	BINDING SITE FOR RESIDUE PEG A 490
14	BC5	SOFTWARE	GLU A:25 , GLY A:26 , LYS A:28 , ARG A:92 , ASN A:103 , GLY A:106	BINDING SITE FOR RESIDUE FMT A 491
15	BC6	SOFTWARE	PHE A:301 , THR A:304	BINDING SITE FOR RESIDUE FMT A 492
16	BC7	SOFTWARE	TYR A:66	BINDING SITE FOR RESIDUE FMT A 493
17	BC8	SOFTWARE	LYS A:338	BINDING SITE FOR RESIDUE FMT A 494
18	BC9	SOFTWARE	ASP A:397 , LYS A:404	BINDING SITE FOR RESIDUE FMT A 495
19	CC1	SOFTWARE	TYR A:394	BINDING SITE FOR RESIDUE FMT A 496
20	CC2	SOFTWARE	ARG A:322 , GLU A:323	BINDING SITE FOR RESIDUE FMT A 497
21	CC3	SOFTWARE	TRP B:349 , SER B:430 , ALA B:431 , GLY B:432 , LYS B:438 , TYR B:440 , HOH B:558 , HOH B:605 , HOH B:702 , HOH B:743	BINDING SITE FOR RESIDUE SO4 B 478
22	CC4	SOFTWARE	ARG B:295 , LYS B:298 , HOH B:540	BINDING SITE FOR RESIDUE SO4 B 479
23	CC5	SOFTWARE	ARG B:437	BINDING SITE FOR RESIDUE SO4 B 480
24	CC6	SOFTWARE	PHE B:292 , GLU B:294 , LYS B:297	BINDING SITE FOR RESIDUE PEG B 481
25	CC7	SOFTWARE	ASN B:7 , LEU B:417 , MSE B:418	BINDING SITE FOR RESIDUE PEG B 482
26	CC8	SOFTWARE	ASP B:348 , TRP B:349	BINDING SITE FOR RESIDUE PEG B 483
27	CC9	SOFTWARE	PHE B:301 , THR B:304 , HOH B:491	BINDING SITE FOR RESIDUE PEG B 484
28	DC1	SOFTWARE	ALA B:344 , PHE B:378 , HOH B:670 , HOH B:711 , HOH B:735	BINDING SITE FOR RESIDUE PEG B 485
29	DC2	SOFTWARE	PHE B:81 , LYS B:82 , TYR B:120 , GLY B:121 , HOH B:684	BINDING SITE FOR RESIDUE PEG B 486
30	DC3	SOFTWARE	GLY B:42 , VAL B:43 , THR B:433 , HOH B:559	BINDING SITE FOR RESIDUE FMT B 487
31	DC4	SOFTWARE	PRO B:340	BINDING SITE FOR RESIDUE FMT B 488
32	DC5	SOFTWARE	ASP B:346	BINDING SITE FOR RESIDUE FMT B 489

(no "SS Bond" information available for 3PN8)

(no "Cis Peptide Bond" information available for 3PN8)

(no "SAP(SNP)/Variant" information available for 3PN8)

(no "PROSITE Motif" information available for 3PN8)

(no "Exon" information available for 3PN8)

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:478
 aligned with Q8DT00_STRMU | Q8DT00 from UniProtKB/TrEMBL  Length:477

    Alignment length:478
                             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        
         Q8DT00_STRMU     - -MSKLPENFLWGGAVAAHQLEGGWQEGGKGISVADVMTAGRHGVAREITAGVLEGKYYPNHEAIDFYHHYKEDVKLFAEMGFKCFRTSIAWTRIFPKGDEAEPNEAGLQFYDDLFDECLKYGIEPVVTLSHFELPYHLVTEYGGFTNRKVIDFFVHFAEVCFRRYKDKVKYWMTFNEINNQANYQEDFAPFTNSGIVYKEGDDREAIMYQAAHYELVASARAVKIGHAINPNLNIGCMVAMCPIYPATCNPKDILMAQKAMQKRYYFADVHVHGFYPEHIFKYWERKAIKVDFTERDKKDLFEGTVDYIGFSYYMSFVIDAHRENNPYYDYLETEDLVKNPYVKASDWDWQIDPQGLRYALNWFTDMYHLPLFIVENGFGAIDQVEADGMVHDDYRIDYLGAHIKEMIKAVDEDGVELMGYTPWGCIDLVSAGTGEMRKRYGFIYVDKDDEGKGTLKRSPKLSFNWYKEVIASNGDDI 477
               SCOP domains d3pn8a_ 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....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...eee...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhh...eeeee....eee.................ee...............hhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhhhhhhhh....eeee......................eee...........eeehhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pn8 A   0 AmSKLPENFLWGGAVAAHQLEGGWQEGGKGISVADVmTAGRHGVAREITAGVLEGKYYPNHEAIDFYHHYKEDVKLFAEmGFKCFRTSIAWTRIFPKGDEAEPNEAGLQFYDDLFDECLKYGIEPVVTLSHFELPYHLVTEYGGFTNRKVIDFFVHFAEVCFRRYKDKVKYWmTFNEINNQANYQEDFAPFTNSGIVYKEGDDREAImYQAAHYELVASARAVKIGHAINPNLNIGCmVAmCPIYPATCNPKDILmAQKAmQKRYYFADVHVHGFYPEHIFKYWERKAIKVDFTERDKKDLFEGTVDYIGFSYYmSFVIDAHRENNPYYDYLETEDLVKNPYVKASDWDWQIDPQGLRYALNWFTDmYHLPLFIVENGFGAIDQVEADGmVHDDYRIDYLGAHIKEmIKAVDEDGVELmGYTPWGCIDLVSAGTGEmRKRYGFIYVDKDDEGKGTLKRSPKLSFNWYKEVIASNGDDI 477
                             |       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        
                             |                                 36-MSE                                     79-MSE                                                                                      172-MSE                            207-MSE                       237-MSE           255-MSE|                                                   314-MSE                                             366-MSE                389-MSE          406-MSE     418-MSE           436-MSE                                     
                             1-MSE                                                                                                                                                                                                                                        240-MSE             260-MSE

Chain B from PDB  Type:PROTEIN  Length:477
 aligned with Q8DT00_STRMU | Q8DT00 from UniProtKB/TrEMBL  Length:477

    Alignment length:477
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       
         Q8DT00_STRMU     1 MSKLPENFLWGGAVAAHQLEGGWQEGGKGISVADVMTAGRHGVAREITAGVLEGKYYPNHEAIDFYHHYKEDVKLFAEMGFKCFRTSIAWTRIFPKGDEAEPNEAGLQFYDDLFDECLKYGIEPVVTLSHFELPYHLVTEYGGFTNRKVIDFFVHFAEVCFRRYKDKVKYWMTFNEINNQANYQEDFAPFTNSGIVYKEGDDREAIMYQAAHYELVASARAVKIGHAINPNLNIGCMVAMCPIYPATCNPKDILMAQKAMQKRYYFADVHVHGFYPEHIFKYWERKAIKVDFTERDKKDLFEGTVDYIGFSYYMSFVIDAHRENNPYYDYLETEDLVKNPYVKASDWDWQIDPQGLRYALNWFTDMYHLPLFIVENGFGAIDQVEADGMVHDDYRIDYLGAHIKEMIKAVDEDGVELMGYTPWGCIDLVSAGTGEMRKRYGFIYVDKDDEGKGTLKRSPKLSFNWYKEVIASNGDDI 477
               SCOP domains d3pn8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Glyco_hydro_1-3pn8B01 B:1-475                                                                                                                                                                                                                                                                                                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_1-3pn8B02 B:1-475                                                                                                                                                                                                                                                                                                                                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author ........eeeee.hhhhhh...hhhhh..hhhhhh...........................hhhhhhhhhhhhhhhhh..eeeee.hhhhhh........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...eee...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhh...eeeee....eee.................ee.....ee.....ee.hhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhhhhhhhh....eeee......................eee...........eeehhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pn8 B   1 mSKLPENFLWGGAVAAHQLEGGWQEGGKGISVADVmTAGRHGVAREITAGVLEGKYYPNHEAIDFYHHYKEDVKLFAEmGFKCFRTSIAWTRIFPKGDEAEPNEAGLQFYDDLFDECLKYGIEPVVTLSHFELPYHLVTEYGGFTNRKVIDFFVHFAEVCFRRYKDKVKYWmTFNEINNQANYQEDFAPFTNSGIVYKEGDDREAImYQAAHYELVASARAVKIGHAINPNLNIGCmVAmCPIYPATCNPKDILmAQKAmQKRYYFADVHVHGFYPEHIFKYWERKAIKVDFTERDKKDLFEGTVDYIGFSYYmSFVIDAHRENNPYYDYLETEDLVKNPYVKASDWDWQIDPQGLRYALNWFTDmYHLPLFIVENGFGAIDQVEADGmVHDDYRIDYLGAHIKEmIKAVDEDGVELmGYTPWGCIDLVSAGTGEmRKRYGFIYVDKDDEGKGTLKRSPKLSFNWYKEVIASNGDDI 477
                            |       10        20        30     |  40        50        60        70        80        90       100       110       120       130       140       150       160       170 |     180       190       200      |210       220       230      |240       250    |  260       270       280       290       300       310   |   320       330       340       350       360     | 370       380       390       400     | 410       420       430     | 440       450       460       470       
                            1-MSE                             36-MSE                                     79-MSE                                                                                      172-MSE                            207-MSE                       237-MSE           255-MSE|                                                   314-MSE                                             366-MSE                389-MSE          406-MSE     418-MSE           436-MSE                                     
                                                                                                                                                                                                                                                                         240-MSE             260-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

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)

Streptococcus mutans [TaxId: 1309] (2)

1a	d3pn8a_	A:
1b	d3pn8b_	B:

(no "CATH Domain" information available for 3PN8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_1 (36)

Streptococcus mutans (1)

1a	Glyco_hydro_1-3pn8B01	B:1-475
1b	Glyco_hydro_1-3pn8B02	B:1-475

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8DT00_STRMU | Q8DT00)

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.

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	Q8DT00_STRMU \| Q8DT00	:	4f66 4f79 4gpn

(no "Related Entries Specified in the PDB File" available for 3PN8)

Description

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Ligands, Modified Residues, Ions (4, 62)

Sites (32, 32)

SS Bonds (0, 0)

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