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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ALPHA-GLUCOSIDASE (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174
 
Authors :  K. Tan, C. Tesar, L. Freeman, R. Wilton, G. Babnigg, A. Joachimiak, Midw Center For Structural Genomics (Mcsg)
Date :  13 May 10  (Deposition) - 23 Jun 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Tesar, R. Wilton, L. Keigher, G. Babnigg, A. Joachimiak
The Crystal Structure Of The Alpha-Glucosidase (Family 31) From Ruminococcus Obeum Atcc 29174
Faseb J. V. 24 3939 2010
PubMed-ID: 20581222  |  Reference-DOI: 10.1096/FJ.10-156257

(-) Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PRK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RUMOBE_03919
    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  (2, 57)

Asymmetric/Biological Unit (2, 57)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE54Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:169 , ASP A:197 , ASP A:307 , HOH A:1079BINDING SITE FOR RESIDUE GOL A 664
2AC2SOFTWARETRP B:169 , ASP B:197 , ILE B:198 , ILE B:234 , ASP B:307 , HOH B:719 , HOH B:731BINDING SITE FOR RESIDUE GOL B 664
3AC3SOFTWARETYR B:5 , ARG B:6 , GLU B:25 , HOH B:1032BINDING SITE FOR RESIDUE GOL B 665

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N04)

(-) 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 3N04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N04)

(-) Exons   (0, 0)

(no "Exon" information available for 3N04)

(-) 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:664
 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.......hhhhh....ee..eeeee....eeeeee....eeeee......eeeeee....eeeeee...hhhhhhhhhhhhhh.....hhhhhh.eeee....hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhh...eeeeeee..ee....hhhhhhhhhh.............eee..eeee.....hhhhhhhhhhhhhhhhh....eeeee.......eehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee..ee.hhhhh.eeeeee.....hhhhhhhhhhhhhhhh....eeee...ee...hhhhhhhhhhhhh.....eeee.ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhh....hhhhh...eee...eee.........eeeeee...eeeeee.....eeeeee..eeeeee.....eeeeee...eeee.....hhhhh.....eeee....eeeee..........hhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n04 A   0 AmIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYImDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRmDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDmIYmDIDYmQDFKDFTVNEKNFPDFPEFVKEmKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDmLNPEARKWFGDKYRFLIDQGIEGFWNDmNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAmQAKmKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNmTRAAGEAFERIDPEKRFLmFSRSSYIGmHRYGGIWmGDNKSWWSHILLNLKmLPSLNmCGFmYTGADLGGFGDDTTRDLLLRFLALGVFTPLmRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYmKAALNDDmYFKPLGFVYPDDKmAIRVEDQLmLGNEImIAPVYEQNARGRYVYLPEEmKFIKFmPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENmQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 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    
                             |                                         44-MSE                                                                   118-MSE                                                                    193-MSE   |                    224-MSE                                                 280-MSE                     308-MSE                            343-MSE                                382-MSE            401-MSE  410-MSE 418-MSE         434-MSE |   |                            475-MSE                                  516-MSE 524-MSE       538-MSE  547-MSE |                 573-MSE |                                                630-MSE                             
                             1-MSE                                                                                                                                                                                            196-MSE|                                                                                                                                               347-MSE                                                                                      440-MSE                                                                                                          553-MSE                   579-MSE                                                                                
                                                                                                                                                                                                                                   201-MSE                                                                                                                                                                                                                                            444-MSE                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:664
 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_2-3n04B01 B:47-112                                  --------------------Glyco_hydro_31-3n04B03 B:133-613                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------Gal_mutarotas_2-3n04B02 B:47-112                                  --------------------Glyco_hydro_31-3n04B04 B:133-613                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee.......................eee....eeeeee.....eeee............eeeee.......hhhhh....ee..eeeee....eeeeee....eeeee......eeeeee....eeeeee...hhhhhhhhhhhhh......hhhhhh.eeee....hhhhhhhhhhhhhh......eeeehhhhh..............hhhhhhhhhhh...eeeeeee..ee....hhhhhhhhhh.............eee..eeee.....hhhhhhhhhhhhhhhhh....eeeee.......eehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee..ee.hhhhh.eeeeee....hhhhhhhhhhhhhhhhh....eeee...ee...hhhhhhhhhhhhh.....eeee.ee....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh....hhhhh...eee...eee.........eeeeee...eeeeee.....eeeeee..eeeeee.....eeeeee...eeee.....hhhhh.....eeee....eeeee..........hhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n04 B   0 AmIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYImDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRmDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDmIYmDIDYmQDFKDFTVNEKNFPDFPEFVKEmKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDmLNPEARKWFGDKYRFLIDQGIEGFWNDmNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAmQAKmKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNmTRAAGEAFERIDPEKRFLmFSRSSYIGmHRYGGIWmGDNKSWWSHILLNLKmLPSLNmCGFmYTGADLGGFGDDTTRDLLLRFLALGVFTPLmRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYmKAALNDDmYFKPLGFVYPDDKmAIRVEDQLmLGNEImIAPVYEQNARGRYVYLPEEmKFIKFmPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENmQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 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    
                             1-MSE                                     44-MSE                                                                   118-MSE                                                                    193-MSE   |                    224-MSE                                                 280-MSE                     308-MSE                            343-MSE                                382-MSE            401-MSE  410-MSE 418-MSE         434-MSE |   |                            475-MSE                                  516-MSE 524-MSE       538-MSE  547-MSE |                 573-MSE |                                                630-MSE                             
                                                                                                                                                                                                                              196-MSE|                                                                                                                                               347-MSE                                                                                      440-MSE                                                                                                          553-MSE                   579-MSE                                                                                
                                                                                                                                                                                                                                   201-MSE                                                                                                                                                                                                                                            444-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3N04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N04)

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        A5ZY13_9FIRM | A5ZY13: 3m46 3m6d 3mkk 3nsx 3nuk 3pha 3poc

(-) Related Entries Specified in the PDB File

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