1PBG - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE THREE-DIMENSIONAL STRUCTURE OF 6-PHOSPHO-BETA GALACTOSIDASE FROM LACTOCOCCUS LACTIS

Authors :   C. Wiesmann, G. E. Schulz

Date :   14 Sep 95 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Hydrolase (Glycosyl Hydrolase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Wiesmann, G. Beste, W. Hengstenberg, G. E. Schulz
The Three-Dimensional Structure Of 6-Phospho-Beta-Galactosidase From Lactococcus Lactis.
Structure V. 3 961 1995
PubMed-ID: 8535789 | Reference-DOI: 10.1016/S0969-2126(01)00230-1
(for further references see the PDB file header)

Molecule 1 - 6-PHOSPHO-BETA-D-GALACTOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.85
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	LACG
	Expression System Plasmid	:	PNZ316
	Expression System Taxid	:	562
	Gene	:	LACG
	Organism Scientific	:	LACTOCOCCUS LACTIS
	Organism Taxid	:	1358
	Other Details	:	PRECIPITANT POLYETHYLENE GLYCOL
	Other Details - Source	:	DELTA H DELTA 1TRP
	Strain	:	SUBSP. LACTIS 712
	Synonym	:	PGAL

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:428 , LYS A:435 , HOH A:644	BINDING SITE FOR RESIDUE SO4 A 469
2	AC2	SOFTWARE	SER B:428 , SER B:430 , ASN B:431 , TYR B:437	BINDING SITE FOR RESIDUE SO4 B 469

(no "SS Bond" information available for 1PBG)

Asymmetric Unit

No.	Residues
1	Glu A:47	-	Pro A:48
2	Pro A:175	-	Pro A:176
3	Trp A:421	-	Ser A:422
4	Glu B:47	-	Pro B:48
5	Pro B:175	-	Pro B:176
6	Trp B:421	-	Ser B:422

(no "SAP(SNP)/Variant" information available for 1PBG)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	LACG_LACLL	9-23	2	A:9-23 B:9-23
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	LACG_LACLL	371-379	2	A:371-379 B:371-379

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	LACG_LACLL	9-23	1	A:9-23 -
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	LACG_LACLL	371-379	1	A:371-379 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	LACG_LACLL	9-23	1	- B:9-23
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	LACG_LACLL	371-379	1	- B:371-379

(no "Exon" information available for 1PBG)

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:454
 aligned with LACG_LACLL | P11546 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:468
                                    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        
           LACG_LACLL     1 MTKTLPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWYTAEPASDFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECHKRHVEPFVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWTTFNEIGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLNDFLGINYYMSDWMQAFDGETEIIHNGKGEKGSSKYQIKGVGRRVAPDYVPRTDWDWIIYPEGLYDQIMRVKNDYPNYKKIYITENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE 468
               SCOP domains d1pbga_ A: 6-phospho-beta-D-galactosidase, PGAL                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1pbgA00 A:1-468 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee..hhhh............hhhhhhhhh..........hhhhhhhhhhhhhhh...eeeee..hhhh.........hhhhhhhhhhhhhhhhh..eeeee.......hhhhh..hhh.hhhhhhhhhhhhhhhhh.....eee....hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eee.....hhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhh.....eeeee....eee..........----------..................----....hhhhhhhhhhhhhh......eeeee................hhhhhhhhhhhhhhhhhhh....eeeeee...................eeee....eeee.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLYCOSYL_HYDROL-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pbg A   1 MTKTLPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWYTAEPASDFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECHKRHVEPFVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWTTFNEIGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLNDFLGINYYMSDWMQAFDGETEII----------KYQIKGVGRRVAPDYVPR----WIIYPEGLYDQIMRVKNDYPNYKKIYITENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE 468
                                    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   |     -    |  330       340 |    |350       360       370       380       390       400       410       420       430       440       450       460        
                                                                                                                                                                                                                                                                                                                                                   314        325              342  347

Chain B from PDB  Type:PROTEIN  Length:456
 aligned with LACG_LACLL | P11546 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:468
                                    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        
           LACG_LACLL     1 MTKTLPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWYTAEPASDFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECHKRHVEPFVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWTTFNEIGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLNDFLGINYYMSDWMQAFDGETEIIHNGKGEKGSSKYQIKGVGRRVAPDYVPRTDWDWIIYPEGLYDQIMRVKNDYPNYKKIYITENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE 468
               SCOP domains d1pbgb_ B: 6-phospho-beta-D-galactosidase, PGAL                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1pbgB00 B:1-468 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee..hhhh............hhhhhhhhh..........hhhhhhhhhhhhhh....eeeee..hhhh.........hhhhhhhhhhhhhhhhh..eeeee.......hhhhh..hhh.hhhhhhhhhhhhhhhhh.....eee....hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eee.....hhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhh.....eeeee....eeee......eee.--------.eee.....eee.......----....hhhhhhhhhhhhhh......eeeee................hhhhhhhhhhhhhhhhhhh....eeeeee...................eeee....eeee.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLYCOSYL_HYDROL-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pbg B   1 MTKTLPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWYTAEPASDFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECHKRHVEPFVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWTTFNEIGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPTKYPYDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLNDFLGINYYMSDWMQAFDGETEIIH--------SKYQIKGVGRRVAPDYVPR----WIIYPEGLYDQIMRVKNDYPNYKKIYITENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE 468
                                    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    |    -   |   330       340 |    |350       360       370       380       390       400       410       420       430       440       450       460        
                                                                                                                                                                                                                                                                                                                                                    315      324               342  347

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 '\|'

Asymmetric Unit

Classes(

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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: Family 1 of glycosyl hydrolase (102)

Protein domain: 6-phospho-beta-D-galactosidase, PGAL (4)

Lactococcus lactis [TaxId: 1358] (4)

1a	d1pbga_	A:
1b	d1pbgb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Lactococcus lactis. Organism_taxid: 1358. Strain: subsp. Lactis 712. (4)

1a	1pbgA00	A:1-468
1b	1pbgB00	B:1-468

(no "Pfam Domain" information available for 1PBG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LACG_LACLL | P11546)

molecular function
	GO:0033920	6-phospho-beta-galactosidase activity	Catalysis of the reaction: a 6-phospho-beta-D-galactoside + H2O = 6-phospho-D-galactose + an alcohol.
	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:0005990	lactose catabolic process	The chemical reactions and pathways resulting in the breakdown of lactose, the disaccharide galactopyranosyl-glucose.
	GO:0019512	lactose catabolic process via tagatose-6-phosphate	The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate.
	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
		Glu A:47 - Pro A:48	[ RasMol ]
		Glu B:47 - Pro B:48	[ RasMol ]
		Pro A:175 - Pro A:176	[ RasMol ]
		Pro B:175 - Pro B:176	[ RasMol ]
		Trp A:421 - Ser A:422	[ RasMol ]
		Trp B:421 - Ser B:422	[ RasMol ]

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	1pbg
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	LACG_LACLL \| P11546	:	2pbg 3pbg 4pbg

(no "Related Entries Specified in the PDB File" available for 1PBG)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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