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(-) Description

Title :  CRYSTAL STRUCTURE OF APO AGD31B, ALPHA-TRANSGLUCOSYLASE IN GLYCOSIDE HYDROLASE FAMILY 31
 
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 :  1.90
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

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2OXL1Ligand/IonOXALATE ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO410Ligand/IonSULFATE ION
Biological Unit 1 (4, 36)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2OXL2Ligand/IonOXALATE ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4SO420Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:323 , PRO A:324 , LEU A:325 , ASP A:326 , HOH A:2249 , HOH A:2251 , HOH A:2256 , HOH A:2259BINDING SITE FOR RESIDUE SO4 A1818
02AC2SOFTWAREASP A:553 , GLU A:554 , ARG A:797 , HOH A:2424 , HOH A:2643BINDING SITE FOR RESIDUE SO4 A1819
03AC3SOFTWAREARG A:58 , ARG A:231 , HOH A:2019BINDING SITE FOR RESIDUE SO4 A1820
04AC4SOFTWARETHR A:732 , ASP A:733 , ASN A:734 , HOH A:2579BINDING SITE FOR RESIDUE SO4 A1821
05AC5SOFTWAREASP A:124 , GLY A:239 , ASN A:240 , SER A:244 , ASN A:248BINDING SITE FOR RESIDUE SO4 A1822
06AC6SOFTWARETHR A:97 , GLU A:98 , ASN A:99 , HIS A:100 , GLN A:703BINDING SITE FOR RESIDUE SO4 A1823
07AC7SOFTWARETHR A:648 , ASP A:649 , GLY A:650 , ALA A:651BINDING SITE FOR RESIDUE SO4 A1824
08AC8SOFTWAREARG A:274 , HOH A:2225BINDING SITE FOR RESIDUE SO4 A1825
09AC9SOFTWARESER A:63 , GLU A:64 , GLN A:251BINDING SITE FOR RESIDUE SO4 A1826
10BC1SOFTWARELYS A:360 , GLU A:809 , ALA A:810 , HOH A:2581BINDING SITE FOR RESIDUE SO4 A1827
11BC2SOFTWARESER A:764 , ARG A:798 , LYS A:817 , HOH A:2598 , HOH A:2645BINDING SITE FOR RESIDUE OXL A1828
12BC3SOFTWAREGLN A:77 , LEU A:78 , GLY A:230 , THR A:432BINDING SITE FOR RESIDUE EDO A1829
13BC4SOFTWAREARG A:685BINDING SITE FOR RESIDUE EDO A1830
14BC5SOFTWAREARG A:561 , PRO A:562 , LYS A:565 , HOH A:2430BINDING SITE FOR RESIDUE EDO A1831
15BC6SOFTWARELYS A:358 , ARG A:753 , ARG A:808 , GLU A:809 , HOH A:2244BINDING SITE FOR RESIDUE EDO A1832
16BC7SOFTWARELEU A:566 , ARG A:569 , TYR A:674 , GLU A:690 , HOH A:2647BINDING SITE FOR RESIDUE PG4 A1833
17BC8SOFTWAREHIS A:178 , HIS A:184 , GLY A:186BINDING SITE FOR RESIDUE EDO A1834
18BC9SOFTWARETHR A:743 , GLY A:744BINDING SITE FOR RESIDUE EDO A1835

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:784 -A:792

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4B9Y)

(-) Sequences/Alignments

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:780
 aligned with OL4AG_CELJU | B3PEE6 from UniProtKB/Swiss-Prot  Length:816

    Alignment length:783
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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 ...eeeeee....eeeee..eeeeeeeee..eeeeee.....................eeee...eeeee...eeeeee....eeeeee..eeeeeeeeeee.---.eeeeee......eeeee..........eeeee.................eeeeeee...eeeee.....eeeee......eeeeee.....eeeeee..hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhh.....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............eeee....eeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9y A  35 AVFYKEHKLRNDGLVITTNQGNIRLQFKSEAAIEVLYRADSKQLPSFALAQPESAIKAQLTETENHLQFSGGTLTARIQKRPFAISYYRDSELLLAEESGFQV---KINFRFYLSPGEKILGGGQRILGMDRRGQRFPLYNRAHYGYSDHSGQMYFGLPAIMSSKQYILVFDNSASGAMDIGKTESDILQLEAKSGRSAYILVAGNSYPSLIENFTQVTGRQPLPPRWALGSFASRFGYRSEAETRATVQKYKTEDFPLDTIVLDLYWFGKDIKGHMGNLDWDKENFPTPLDMMADFKQQGVKTVLITEPFVLTSSKRWDDAVKAKALAKDPQGQPKAFELYFGNGGIIDVFSKEGSRWFSSIYKDLSKQGVAGWWGDLGEPEMHPEDTQHAIGDADTVHNAYGHRWAEMLYQQQLDQFPELRPFIMMRAGFVGSQRYGMIPWTGDVSRTWGGLASQVELALQMSLLGFGYIHSDLGGFADGETLDKEMYIRWLQYGVFQPVYRPHGQDHIPSEPVFQDEETKAILRPLVKLRYRMLPYIYTAAYQNTLTGMPLMRPLFFSDEKNPALIDNKTSYFWGDSLLVTPITQAGVESVSIPAPKGVWFDFWKDTRYQTDGAPLTLPTDLHTIPVLVKAGAFMPYVPAVSTTEDYRSDSLEIHYYADASVPLAQGEIFEDDGKDPNSIKRNQFDLLTLQATHTDNQLHFQLARTGKGYRGMPERRATTLVIHNASDQYQHLDINGKTIAIAQADCASTPALACYDQERRQLQLVFTWGREALNLRLHK 817
                                    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   
                                                                                                                                137 141
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4B9Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B9Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B9Y)

(-) Gene Ontology  (7, 7)

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.

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 Related Entries

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        OL4AG_CELJU | B3PEE6: 4b9z 4ba0 5i23 5i24

(-) Related Entries Specified in the PDB File

4b9z CRYSTAL STRUCTURE OF AGD31B, ALPHA-TRANSGLUCOSYLASE, COMPLEXED WITH ACARBOSE
4ba0 CRYSTAL STRUCTURE OF AGD31B, ALPHA-TRANSGLUCOSYLASE, COMPLEXED WITH 5F-ALPHA-GLCF