4BA0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF AGD31B, ALPHA-TRANSGLUCOSYLASE, COMPLEXED WITH 5F-ALPHA-GLCF

Authors :   J. Larsbrink, A. Izumi, G. R. Hemsworth, G. J. Davies, H. Brumer

Date :   09 Sep 12 (Deposition) - 14 Nov 12 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

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

Reference :   J. Larsbrink, A. Izumi, G. R. Hemsworth, G. J. Davies, H. Brumer
Structural Enzymology Of Cellvibrio Japonicus Agd31B Reveals Alpha-Transglucosylase Activity In Glycoside Hydrolase Family 31
J. Biol. Chem. V. 287 43288 2012
PubMed-ID: 23132856 | Reference-DOI: 10.1074/JBC.M112.416511

Molecule 1 - ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B
	Chains	:	A
	EC Number	:	3.2.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PENTR/SD/D-TOPO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CELLVIBRIO JAPONICUS
	Organism Taxid	:	155077
	Synonym	:	ALPHA-TRANSGLUCOSYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 12)

No.	Name	Count	Type	Full Name
1	5GF	1	Ligand/Ion	5-FLUORO-BETA-D-GLUCOPYRANOSE
2	ARG	1	Mod. Amino Acid	ARGININE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
6	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (6, 24)

No.	Name	Count	Type	Full Name
1	5GF	2	Ligand/Ion	5-FLUORO-BETA-D-GLUCOPYRANOSE
2	ARG	2	Mod. Amino Acid	ARGININE
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
6	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:271 , ASP A:299 , ILE A:341 , TRP A:410 , ASP A:412 , ARG A:463 , TRP A:477 , ASP A:480 , PHE A:513 , HIS A:540 , HOH A:2233 , HOH A:2308 , HOH A:2310	BINDING SITE FOR RESIDUE 5GF A1818
02	AC2	SOFTWARE	GLN A:77 , LEU A:78 , SER A:229 , GLY A:230	BINDING SITE FOR RESIDUE EDO A1819
03	AC3	SOFTWARE	ASP A:553 , GLU A:554 , ARG A:797 , HOH A:2358	BINDING SITE FOR RESIDUE SO4 A1820
04	AC4	SOFTWARE	ARG A:561 , PRO A:562 , LYS A:565 , HOH A:2365 , HOH A:2555	BINDING SITE FOR RESIDUE SO4 A1821
05	AC5	SOFTWARE	THR A:323 , PRO A:324 , LEU A:325 , ASP A:326 , HOH A:2216 , HOH A:2217 , HOH A:2220 , HOH A:2222	BINDING SITE FOR RESIDUE SO4 A1822
06	AC6	SOFTWARE	ARG A:58 , ARG A:231 , HOH A:2015	BINDING SITE FOR RESIDUE SO4 A1823
07	AC7	SOFTWARE	THR A:732 , ASP A:733 , ASN A:734 , GLN A:735	BINDING SITE FOR RESIDUE SO4 A1824
08	AC8	SOFTWARE	ARG A:123 , GLY A:239 , ASN A:240 , SER A:244 , ASN A:248	BINDING SITE FOR RESIDUE SO4 A1825
09	AC9	SOFTWARE	THR A:97 , GLU A:98 , ASN A:99 , HIS A:100 , GLN A:703	BINDING SITE FOR RESIDUE SO4 A1826
10	BC1	SOFTWARE	ARG A:569 , TYR A:674 , HOH A:2421	BINDING SITE FOR RESIDUE PGE A1827
11	BC2	SOFTWARE	HIS A:731 , THR A:732 , ASP A:733 , GLN A:735 , SER A:764 , TYR A:767 , LYS A:817 , HOH A:2512 , HOH A:2556	BINDING SITE FOR RESIDUE PEG A1828
12	BC3	SOFTWARE	ARG A:176 , ALA A:177 , HIS A:178 , GLN A:187	BINDING SITE FOR RESIDUE ARG A1829

Asymmetric Unit

No.	Residues
1	A:784	-	A:792

Asymmetric Unit

No.	Residues
1	Arg A:44	-	Asn A:45
2	Asn A:45	-	Asp A:46
3	Arg A:115	-	Pro A:116
4	Phe A:271	-	Gly A:272
5	Glu A:415	-	Pro A:416

(no "SAP(SNP)/Variant" information available for 4BA0)

(no "PROSITE Motif" information available for 4BA0)

(no "Exon" information available for 4BA0)

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:782
 aligned with OL4AG_CELJU | B3PEE6 from UniProtKB/Swiss-Prot  Length:816

    Alignment length:784
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       816  
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814 |  
         OL4AG_CELJU     35 AVFYKEHKLRNDGLVITTNQGNIRLQFKSEAAIEVLYRADSKQLPSFALAQPESAIKAQLTETENHLQFSGGTLTARIQKRPFAISYYRDSELLLAEESGFQVNTDKINFRFYLSPGEKILGGGQRILGMDRRGQRFPLYNRAHYGYSDHSGQMYFGLPAIMSSKQYILVFDNSASGAMDIGKTESDILQLEAKSGRSAYILVAGNSYPSLIENFTQVTGRQPLPPRWALGSFASRFGYRSEAETRATVQKYKTEDFPLDTIVLDLYWFGKDIKGHMGNLDWDKENFPTPLDMMADFKQQGVKTVLITEPFVLTSSKRWDDAVKAKALAKDPQGQPKAFELYFGNGGIIDVFSKEGSRWFSSIYKDLSKQGVAGWWGDLGEPEMHPEDTQHAIGDADTVHNAYGHRWAEMLYQQQLDQFPELRPFIMMRAGFVGSQRYGMIPWTGDVSRTWGGLASQVELALQMSLLGFGYIHSDLGGFADGETLDKEMYIRWLQYGVFQPVYRPHGQDHIPSEPVFQDEETKAILRPLVKLRYRMLPYIYTAAYQNTLTGMPLMRPLFFSDEKNPALIDNKTSYFWGDSLLVTPITQAGVESVSIPAPKGVWFDFWKDTRYQTDGAPLTLPTDLHTIPVLVKAGAFMPYVPAVSTTEDYRSDSLEIHYYADASVPLAQGEIFEDDGKDPNSIKRNQFDLLTLQATHTDNQLHFQLARTGKGYRGMPERRATTLVIHNASDQYQHLDINGKTIAIAQADCASTPALACYDQERRQLQLVFTWGREALNLRLH--    -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee..eeeeeeeee..eeeeee.....................eeee...eeeee...eeeeee....eeeeee..eeeeeeeeeee..--.eeeeee......eeeee..........eeeee.................eeeeeee...eeeee.....eeeee......eeeeee.....eeeeee..hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhhh....eeeehhhhh...................hhhhhhhhhhhh..eeeeee..eee....hhhhhhhh.............eee..eeeee....hhhhhhhhhhhhhhhhhhh..eeee............ee..eehhhhh.hhhhhhhhhhhhhhhhhh......eee.....hhhhh.eee.......hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhh..hhhhhhh...eee...eee.........eeee....eeeee.....eeee....eeee.......eeee...eeee.....hhhhh...eeeeeee......eeeeeeee..............eeeeeeeee...eeeeeeeee..........eeeeeeee.......eeee..eeee....hhhhh...eeee....eeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ba0 A   35 AVFYKEHKLRNDGLVITTNQGNIRLQFKSEAAIEVLYRADSKQLPSFALAQPESAIKAQLTETENHLQFSGGTLTARIQKRPFAISYYRDSELLLAEESGFQVN--KINFRFYLSPGEKILGGGQRILGMDRRGQRFPLYNRAHYGYSDHSGQMYFGLPAIMSSKQYILVFDNSASGAMDIGKTESDILQLEAKSGRSAYILVAGNSYPSLIENFTQVTGRQPLPPRWALGSFASRFGYRSEAETRATVQKYKTEDFPLDTIVLDLYWFGKDIKGHMGNLDWDKENFPTPLDMMADFKQQGVKTVLITEPFVLTSSKRWDDAVKAKALAKDPQGQPKAFELYFGNGGIIDVFSKEGSRWFSSIYKDLSKQGVAGWWGDLGEPEMHPEDTQHAIGDADTVHNAYGHRWAEMLYQQQLDQFPELRPFIMMRAGFVGSQRYGMIPWTGDVSRTWGGLASQVELALQMSLLGFGYIHSDLGGFADGETLDKEMYIRWLQYGVFQPVYRPHGQDHIPSEPVFQDEETKAILRPLVKLRYRMLPYIYTAAYQNTLTGMPLMRPLFFSDEKNPALIDNKTSYFWGDSLLVTPITQAGVESVSIPAPKGVWFDFWKDTRYQTDGAPLTLPTDLHTIPVLVKAGAFMPYVPAVSTTEDYRSDSLEIHYYADASVPLAQGEIFEDDGKDPNSIKRNQFDLLTLQATHTDNQLHFQLARTGKGYRGMPERRATTLVIHNASDQYQHLDINGKTIAIAQADCASTPALACYDQERRQLQLVFTWGREALNLRLHKR 1829
                                    44        54        64        74        84        94       104       114       124       134   |  |144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814  ||
                                                                                                                                 138  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 817|
                                                                                                                                    141                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 1829

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 4BA0)

(no "CATH Domain" information available for 4BA0)

(no "Pfam Domain" information available for 4BA0)

Asymmetric Unit(hide GO term definitions)

Chain A (OL4AG_CELJU | B3PEE6)

molecular function
	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:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
	GO:0033825	oligosaccharide 4-alpha-D-glucosyltransferase activity	Catalysis of the transfer of the non-reducing terminal alpha-D-glucose residue from a 1,4-alpha-D-glucan to the 4-position of an alpha-D-glucan, thus bringing about the hydrolysis of oligosaccharides.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		5GF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ARG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Arg A:115 - Pro A:116	[ RasMol ]
		Arg A:44 - Asn A:45	[ RasMol ]
		Asn A:45 - Asp A:46	[ RasMol ]
		Glu A:415 - Pro A:416	[ RasMol ]
		Phe A:271 - Gly A:272	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	4ba0
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	OL4AG_CELJU \| B3PEE6
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	3.2.1.20
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	OL4AG_CELJU \| B3PEE6
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UniProtKB/Swiss-Prot
	OL4AG_CELJU \| B3PEE6	:	4b9y 4b9z 5i23 5i24

4b9y	CRYSTAL STRUCTURE OF APO AGD31B, ALPHA-TRANSGLUCOSYLASE IN GLYCOSIDE HYDROLASE FAMILY 31
4b9z	CRYSTAL STRUCTURE OF AGD31B, ALPHA-TRANSGLUCOSYLASE, COMPLEXED WITH ACARBOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (12, 12)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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