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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE D307A MUTANT OF GLYCOSIDE HYDROLASE (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174
 
Authors :  K. Tan, C. Tesar, L. Freeman, G. Babnigg, A. Joachimiak, Midwest Cente Structural Genomics (Mcsg)
Date :  15 Mar 10  (Deposition) - 21 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Mcsg, Midwest Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Tesar, R. Wilton, L. Keigher, G. Babnigg, A. Joachimiak
Novel Alpha-Glucosidase From Human Gut Microbiome: Substrat Specificities And Their Switch.
Faseb J. V. 24 3939 2010
PubMed-ID: 20581222  |  Reference-DOI: 10.1096/FJ.10-156257

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RUMOBE_03919
    Mutation: YES
    Organism Scientific: RUMINOCOCCUS OBEUM
    Organism Taxid: 411459
    Strain: ATCC 29174

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3M6D)

(-) Sites  (0, 0)

(no "Site" information available for 3M6D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M6D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:310 -Pro A:311
2Glu B:310 -Pro B:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M6D)

(-) Exons   (0, 0)

(no "Exon" information available for 3M6D)

(-) Sequences/Alignments

Asymmetric/Biological 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:655
 aligned with A5ZY13_9FIRM | A5ZY13 from UniProtKB/TrEMBL  Length:663

    Alignment length:664
                             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       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659    
         A5ZY13_9FIRM     - -MIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNDMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGDNKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......................eee....eeeeee.....eeee............eeeee................ee..eeeee...eeeeeee....eeeee......eeeeee....eeeeeee..hhhhhhhhhhhhhh.....hhhhh.eeeee....hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhh...eeeeeee..ee....hhhhhhhhhh.............eee..eeee.....hhhhhhhhhh.hhhhhh....eeeee.......eehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee..ee.hhhhh.eeee......hhhhhhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeee.---------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh....hhhhh...eee...ee...........eeeee...eeeeee.....eeeeee..eeeee......eeeeee...eeee.....hhhhh.....eeee....eeeee..........hhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m6d A   0 AMIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNAMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGDNKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAA---------QFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
                                     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       479|        -|      499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          480       490                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:658
 aligned with A5ZY13_9FIRM | A5ZY13 from UniProtKB/TrEMBL  Length:663

    Alignment length:664
                             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       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659    
         A5ZY13_9FIRM     - -MIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNDMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGDNKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------Gal_mutarotas_2-3m6dB01 B:47-112                                  --------------------Glyco_hydro_31-3m6dB03 B:133-613                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------Gal_mutarotas_2-3m6dB02 B:47-112                                  --------------------Glyco_hydro_31-3m6dB04 B:133-613                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee.......................eee....eeeeee.....eeee............eeeee................ee..eeeee....eeeeee....eeeee......eeeeee....eeeeeee..hhhhhhhhhhhhh......hhhhhh.eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhh..........hhhhhhhhhhh...eeeeeee..ee....hhhhhhhhhh.............ee....eee.....hhhhhhhhhh.hhhhhh....eeeee........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..........eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee..ee.hhhhh.eee......hhhhhhhh..hhhhhhhh....ee..........hhhhhhhhhhhhh.....eeee.------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhh..hhhhhh....eee...eee..........eeeee...eeeeee.....ee..ee..eeeee......eeeeee...eeee...............eeee....eee..................eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m6d B   0 AMIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNAMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGDNKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAA------ECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
                                     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       479|      489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          480    487
   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 3M6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M6D)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Gal_mutarotase (81)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A5ZY13_9FIRM | A5ZY13)
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: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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  Cis Peptide Bonds
    Glu A:310 - Pro A:311   [ RasMol ]  
    Glu B:310 - Pro B:311   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A5ZY13_9FIRM | A5ZY13: 3m46 3mkk 3n04 3nsx 3nuk 3pha 3poc

(-) Related Entries Specified in the PDB File

3ffj 3FFJ IS A D307A MUTANT OF 3FFJ.
3m46 3M46 IS A D73A MUTANT OF 3FFJ. RELATED ID: APC21248 RELATED DB: TARGETDB