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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE THE CRYSTAL STRUCTURE OF THE D420A MUTANT OF THE ALPHA-GLUCOSIDASE (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174
 
Authors :  K. Tan, C. Tesar, R. Wilton, L. Keigher, G. Babnigg, A. Joachimiak, Midw Center For Structural Genomics (Mcsg)
Date :  02 Jul 10  (Deposition) - 21 Jul 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Acarbose, Alpha-Glucose, Structural Complex, 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 The Crystal Structure Of The D420A Mutant Of The Alpha-Glucosidase (Family 31) From Ruminococcus Obeum Atcc 29174
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
    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  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:341 , HOH A:786 , HOH A:1023 , HOH A:1266 , TRP B:271 , PHE B:314BINDING SITE FOR RESIDUE TRS A 664
2AC2SOFTWARETRP A:169 , ASP A:197 , ASP A:307 , HOH A:1068BINDING SITE FOR RESIDUE TRS A 665
3AC3SOFTWAREPHE A:314 , TRP B:341 , HOH B:1055BINDING SITE FOR RESIDUE TRS B 664

(-) SS Bonds  (0, 0)

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

(-) 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 3NSX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NSX)

(-) 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:666
 aligned with A5ZY13_9FIRM | A5ZY13 from UniProtKB/TrEMBL  Length:663

    Alignment length:666
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657      
         A5ZY13_9FIRM     - ---MIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNDMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGDNKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.......................eee....eeeeee.....eeee............eeeee................ee..eeeee....eeeeee....eeeee......eeeeee....eeeeeee..hhhhhhhhhhhhhh.....hhhhh.eeeee....hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhh...eeeeeee..ee....hhhhhhhhhh.............eee..eeee.....hhhhhhhhhhhhhhhhh....eeeee.......eehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee..ee.hhhhh.eeee......hhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhh....eeeee.......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....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
                 3nsx A  -2 SNAMIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNDMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGANKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657      


Chain B from PDB  Type:PROTEIN  Length:666
 aligned with A5ZY13_9FIRM | A5ZY13 from UniProtKB/TrEMBL  Length:663

    Alignment length:666
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657      
         A5ZY13_9FIRM     - ---MIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNDMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGDNKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------Gal_mutarotas_2-3nsxB01 B:47-112                                  --------------------Glyco_hydro_31-3nsxB03 B:133-613                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Gal_mutarotas_2-3nsxB02 B:47-112                                  --------------------Glyco_hydro_31-3nsxB04 B:133-613                                                                                                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeee.......................eee....eeeeee.....eeee............eeeee................ee..eeeee....eeeeee....eeeee......eeeeee....eeeeeee..hhhhhhhhhhhhh......hhhhhh.eeee....hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhh...eeeeeee..ee....hhhhhhhhhh.............eee..eeee.....hhhhhhhhhhhhhhhhh....eeeee.......eehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee..ee.hhhhh.eeee......hhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhh.....eeee.............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
                 3nsx B  -2 SNAMIRKYRYGAPFDTEALTEKIETAEEAFPYGEISQKEGFAFTYIMDEDDIVYGLGESNRGINKRGYCYISNCTDDPIHTEDKRSLYGAHNFIIVSGKTTFGLFFDYPSKLTFDIGYTRMDTLKVSCENADLDIYVIEGENAYDIVKQFRRVIGRSYIPPKFAFGFGQSRWGYTTKEDFRAVAKGYRENHIPIDMIYMDIDYMQDFKDFTVNEKNFPDFPEFVKEMKDQELRLIPIIDAGVKVEKGYEVYEEGVKNNYFCKREDGSDFVAAVWPGDTHFPDMLNPEARKWFGDKYRFLIDQGIEGFWNDMNEPAIFYSSEGLAEAKEFAGEFAKDTEGKIHPWAMQAKMKDIVNSPEDYKRFYHNVNGKKIRHDKVHNLFGYNMTRAAGEAFERIDPEKRFLMFSRSSYIGMHRYGGIWMGANKSWWSHILLNLKMLPSLNMCGFMYTGADLGGFGDDTTRDLLLRFLALGVFTPLMRDHAAEGTREQECYQFENIEDFRSVINARYRLVPYLYSEYMKAALNDDMYFKPLGFVYPDDKMAIRVEDQLMLGNEIMIAPVYEQNARGRYVYLPEEMKFIKFMPDGSISEEVLEKGVHYVDVALNEVPLFIRSGKCIPVAEAAECVKDIDTENMQLIGYEGSSYTLYEDDGIHKDYDKKENYRVLTK 663
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657
   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 3NSX)

(-) CATH Domains  (0, 0)

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

(-) 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 3n04 3nuk 3pha 3poc

(-) Related Entries Specified in the PDB File

3m46 D73A MUTANT RELATED ID: APC21248 RELATED DB: TARGETDB
3m6d D307A MUTANT
3mkk D307A MUTANT IN COMPLEX WITH ISOMALTOSE
3n04 WILD TYPE
3nqq D307A MUTANT IN COMPLEX WITH ACARBOSE