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Title :   CRYSTAL STRUCTURE OF A GLYCOSYL HYDROLASES FAMILY 2 PROTEIN FROM BACTEROIDES THETAIOTAOMICRON

Authors :   D. Kumaran, J. Bonanno, R. Romero, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   09 Jun 08 (Deposition) - 17 Jun 08 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Glucosyl Hydrolase Family 2, Beta-Galactosidase, Nysgxrc, Protein Structure Initiative Ii (Psi-Ii), Jelly-Roll Fold, Immunoglobulin-Like Fold, Tim-Barrel Domain, Structural Genomics, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kumaran, J. Bonanno, R. Romero, S. K. Burley, S. Swaminathan
Crystal Structure Of A Glycosyl Hydrolases Family 2 Protein From Bacteroides Thetaiotaomicron.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - BETA-GALACTOSIDASE
	Atcc	:	29148
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSGX4(BS)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 29-1024
	Gene	:	BT_3179
	Mutation	:	YES
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON VPI-5482
	Organism Taxid	:	226186
	Strain	:	VPI-5482 / DSM 2079 / NCTC 10582 / E50

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 15)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 28)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:900 , LEU A:942 , GLU A:943 , ALA A:945 , HOH A:1102 , HOH A:1103	BINDING SITE FOR RESIDUE K A 1101

Asymmetric Unit

No.	Residues
1	A:498	-	A:523

Asymmetric Unit

No.	Residues
1	Val A:81	-	Pro A:82
2	Pro A:113	-	Pro A:114
3	Ile A:149	-	Ser A:150
4	Trp A:555	-	Asp A:556
5	Gly A:869	-	Glu A:870

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

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

(no "Exon" information available for 3DEC)

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:983
 aligned with Q8A2X6_BACTN | Q8A2X6 from UniProtKB/TrEMBL  Length:1024

    Alignment length:995
                                    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       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019     
        Q8A2X6_BACTN     30 QPEWQSQYAVGLNKLDPHTYVWPYADASEVEKGTFEQSPYYMSLNGQWKFHWVKNPDTRPKDFYKPSYYTGGWADIKVPGNWERQGYGTAIYVNETYEFDDKMFNFKKNPPLVPYKENEVGSYRRTFKVPAGWEGRRVVLCCEGVISFYYVWVNGEFLGYNQGSKTAAEWDITDKLTDGENTIALEVYRWSSGAYLECQDMWRLSGIERDVYLYSTPEQYIADYKVTSLLEKEHYKEGIFELEVAVGGTASGTSSIAYTLKDASDKTVLEGSRKLESHGSGNLIVFDEQRLPDVRRWNAEHPELYTLLLELKDAGGKVTEITGTKVGFRTSEIKNGRFCINGVPVLVKGVNRHEHSQLGRTVSKELMEQDIRLMKQHNINTVRNSHYPAHPYWYQLCDRYGLYVIDEANIESHGMGYGPASLAKDSTWLPAHIDRTRRMYERSKNHPSVVIWSLGNEAGNGINFERTYDWLKSVEKNRPVQYERAEENYNTDIYCRMYRSVDVIRNYVARKDIYRPFILCEYLHAMGNSCGGMKEYWEVFENEPMAQGGCIWDWVDQSFREVDKDGKWYWTYGGDYGPKDVPSFGNFCCNGLVNAVREPHPHLLEVKKIYQNIKSTLIDKKNLTVRVKNWFDFSDLNEYILHWKVTGDDGTVLAEGNKEVACEPHATVELTLGAVQLPKTIREAYLDLGWTRKKSTPLVDTAWEIAYDQFVLPASGKVWNGKPSEAGKTTFEVDENTGALKSLCLDGEELLASPVTISLFRPATDNDNRDRMGAKLWRKAGLHTLTQKVVSLKESKTSATAQVNILNVTGKKVGDATLEYTLNHNGSLKVQTTFQPDTTWVKSIARLGLTFEMNDTYGNVTYLGRGEHETYIDRNQSGKIGIYTTTPEKMFHYYVIPQSTGNRTDVRWVKLADDSGKGCWIESDSPFQFSALPFSDLLLEKALHINDLERNGRITVHLDAKQAGVGTATCGPGVLPPYLVPLGKQTFTFTIYPVK 1024
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3decA01 A:4-221 Galactose-binding domain-like                                                                                                                                                                             3decA02 A:222-332  [code=2.60.4   0.320, no name defined       ]                                               3decA03 A:333-613 Glycosidases                                                                                                                                                                                                                                                           3decA04 A:614-718  [code=2.60.40.320, no name defined]                                                   -----------3decA05 A:730-998  [code=2.70.98.10, no name defined]                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...................hhhhhhhhhhhhh..eee..eeeeeeeee.hhhh..............eeeee..hhhhhh....eee.......hhhhh.............eeeeeeeeee.hhhhh..eeeeee..ee.eeeeee..eeeeeee.....eeee.hhhh...eeeeeeeee..hhhhhhh...eee..ee...eeeeee..eeeeeeeeeeee.......eeeeeeeeeee.---..eeeeeee.....eeeeeee.-------..ee...eee.............eeeeeeee.....eeeeeeeee....eeee..eeee..ee..eeeeee..........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.eeeee........--.......hhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh....eehhhhh.............hhhhhhhhhh.......eeeeee.........hhhhhhhhhh....eeeeee.......eeee.....eeee............hhhhhh..........hhhhhhhhhhhh.eeeeeee....eeeeee.....hhh.eeeeeeeee...eeeeeeee........eeeee...........eeeeeeeeee.............eeeeeeee...............eeeee......eeeeee..ee......eee.....hhhhhhh..hhhhhhhh.....eeeeeeeeee..eeeeeeeee.....eeeeeeeeeee.....eeeeeeeee.........eeeeeeeee....eeeeeeee............eeeeeeehhhhhh...........eeeeeeeeee.....eeeeeeeeeeeeeee..hhhhhhhh.hhhhh....eeeeeeeeee............hhhhh.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3dec A    4 QPEWQSQYAVGLNKLDPHTYVWPYADASEVEKGTFEQSPYYmSLNGQWKFHWVKNPDTRPKDFYKPSYYTGGWADIKVPGNWERQGYGTAIYVNETYEFDDKmFNFKKNPPLVPYKENEVGSYRRTFKVPAGWEGRRVVLCCEGVISFYYVWVNGEFLGYNQGSKTAAEWDITDKLTDGENTIALEVYRWSSGAYLECQDmWRLSGIERDVYLYSTPEQYIADYKVTSLLEKEHYKEGIFELEVAVGGT---TSSIAYTLKDASDKTVLEGSRK-------NLIVFDEQRLPDVRRWNAEHPELYTLLLELKDAGGKVTEITGTKVGFRTSEIKNGRFCINGVPVLVKGVNRHEHSQLGRTVSKELmEQDIRLmKQHNINTVRNSHYPAHPYWYQLCDRYGLYVIDEANIESHGm--GPASLAKDSTWLPAHIDRTRRmYERSKNHPSVVIWSLGNEAGNGINFERTYDWLKSVEKNRPVQYERAEENYNTDIYCRmYRSVDVIRNYVVRKDIYRPFILCEYLHAmGNSCGGmKEYWEVFENEPmAQGGCIWDWVDQSFREVDKDGKWYWTYGGDYGPKDVPSFGNFCCNGLVNAVREPHPHLLEVKKIYQNIKSTLIDKKNLTVRVKNWFDFSDLNEYILHWKVTGDDGTVLAEGNKEVACEPHATVELTLGAVQLPKTIREAYLDLGWTRKKSTPLVDTAWEIAYDQFVLPASGKVWNGKPSEAGKTTFEVDENTGALKSLCLDGEELLASPVTISLFRPATDNDNRDRmGAKLWRKAGLHTLTQKVVSLKESKTSATAQVNILNVTGKKVGDATLEYTLNHNGSLKVQTTFQPDTTWVKSIARLGLTFEmNDTYGNVTYLGRGEHETYIDRNQSGKIGIYTTTPEKmFHYYVIPQSTGNRTDVRWVKLADDSGKGCWIESDSPFQFSALPFSDLLLEKALHINDLERNGRITVHLDAKQAGVGTATCGPGVLPPYLVPLGKQTFTFTIYPVK  998
                                    13        23        33        43 |      53        63        73        83        93       103  |    113       123       133       143       153       163       173       183       193       203|      213       223       233       243        |-  |    263       273   |     - |     293       303       313       323       333       343       353       363      |373   |   383       393       403       413    |  423       433       443       453       463       473       483       493      |503       513       523     | 533  |    543    |  553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773 |     783       793       803       813       823       833       843       853  |    863       873       883       893       903       913       923       933       943       953       963       973       983       993     
                                                                    45-MSE                                                      106-MSE                                                                                           204-MSE                                         252 256                  277     285                                                                                  370-MSE  |                                      418-MSE                 442-MSE                                                   500-MSE                      529-MSE  |         548-MSE                                                                                                                                                                                                                            775-MSE                                                                          856-MSE                              893-MSE                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                               377-MSE                                     421                                                                                                                536-MSE

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 3DEC)

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

Asymmetric Unit(hide GO term definitions)

Chain A (Q8A2X6_BACTN | Q8A2X6)

molecular function
	GO:0004565	beta-galactosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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.
cellular component
	GO:0009341	beta-galactosidase complex	A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.
	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.

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	Cis Peptide Bonds
		Gly A:869 - Glu A:870	[ RasMol ]
		Ile A:149 - Ser A:150	[ RasMol ]
		Pro A:113 - Pro A:114	[ RasMol ]
		Trp A:555 - Asp A:556	[ RasMol ]
		Val A:81 - Pro A:82	[ RasMol ]

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3bga	CRYSTAL STRUCTURE OF BETA-GALACTOSIDASE FROM BACTEROIDES THETAIOTAOMICRON VPI-5482

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (4, 5)

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Gene Ontology (10, 10)

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