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(-) Description

Title :  THE ROLE OF AN INNER LOOP IN THE CATALYTIC MECHANISM OF SOYBEAN BETA-AMYLASE
 
Authors :  Y. N. Kang, M. Adachi, S. Utsumi, B. Mikami
Date :  17 May 04  (Deposition) - 05 Apr 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  (Beta/Alpha)8 Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. N. Kang, A. Tanabe, M. Adachi, S. Utsumi, B. Mikami
Structural Analysis Of Threonine 342 Mutants Of Soybean Beta-Amylase: Role Of A Conformational Change Of The Inner Loop In The Catalytic Mechanism.
Biochemistry V. 44 5106 2005
PubMed-ID: 15794648  |  Reference-DOI: 10.1021/BI0476580

(-) Compounds

Molecule 1 - BETA-AMYLASE
    Chains: A
    EC Number: 3.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-2
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Synonym: 1,4-ALPHA-D-GLUCAN MALTOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3SO48Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:53 , TRP A:55 , HIS A:93 , ASP A:101 , ARG A:420 , BGC A:497 , HOH A:596 , HOH A:629 , HOH A:716 , HOH A:779BINDING SITE FOR RESIDUE GLC A 496
02AC2SOFTWAREALA A:184 , GLU A:186 , LYS A:295 , ALA A:342 , GLU A:380 , ALA A:382 , LEU A:419 , GLC A:496 , HOH A:758 , HOH A:779 , HOH A:1029 , HOH A:1282 , HOH A:1284BINDING SITE FOR RESIDUE BGC A 497
03AC3SOFTWAREVAL A:99 , TRP A:198 , HIS A:300 , MET A:346 , LEU A:383 , HOH A:631 , HOH A:887 , HOH A:1077 , HOH A:1240 , HOH A:1282 , HOH A:1285BINDING SITE FOR RESIDUE GLC A 499
04AC4SOFTWAREHIS A:146 , ARG A:326 , ARG A:330 , ARG A:372 , HOH A:966 , HOH A:1242BINDING SITE FOR RESIDUE SO4 A 2000
05AC5SOFTWAREHIS A:119 , ARG A:130 , HOH A:1066BINDING SITE FOR RESIDUE SO4 A 2001
06AC6SOFTWAREGLY A:225 , LYS A:304 , LYS A:453 , HOH A:1035 , HOH A:1036 , HOH A:1171BINDING SITE FOR RESIDUE SO4 A 2002
07AC7SOFTWAREARG A:347 , SER A:349 , HOH A:611 , HOH A:765 , HOH A:1006 , HOH A:1064BINDING SITE FOR RESIDUE SO4 A 2003
08AC8SOFTWAREGLN A:77 , ARG A:372 , THR A:480 , LEU A:481 , HOH A:627 , HOH A:628 , HOH A:733 , HOH A:872BINDING SITE FOR RESIDUE SO4 A 2004
09AC9SOFTWARETHR A:256 , GLU A:257 , HOH A:610 , HOH A:954 , HOH A:1141BINDING SITE FOR RESIDUE SO4 A 2005
10BC1SOFTWAREASN A:125 , SER A:127 , GLU A:205 , LYS A:237 , HOH A:784 , HOH A:832 , HOH A:838 , HOH A:1001 , HOH A:1032BINDING SITE FOR RESIDUE SO4 A 2006
11BC2SOFTWAREPRO A:352 , SER A:353 , HOH A:788BINDING SITE FOR RESIDUE SO4 A 2007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WDS)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:200 -Pro A:201
2Leu A:419 -Arg A:420

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WDS)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_AMYLASE_1PS00506 Beta-amylase active site 1.AMYB_SOYBN94-102  1A:93-101
2BETA_AMYLASE_2PS00679 Beta-amylase active site 2.AMYB_SOYBN183-193  1A:182-192

(-) Exons   (0, 0)

(no "Exon" information available for 1WDS)

(-) 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:492
 aligned with AMYB_SOYBN | P10538 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:492
                                    14        24        34        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  
           AMYB_SOYBN     5 DSNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLFQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPRIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNAKPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 496
               SCOP domains -d1wdsa1 A:5-495 beta-Amylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1wdsA00 A:4-495 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -----------Glyco_hydro_14-1wdsA01 A:15-437                                                                                                                                                                                                                                                                                                                                                                                                        ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....eeee.............hhhhhhhhhhhhhhh...eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhh...eee.....eeeeee.hhhh........hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhh......hhhhh............hhhhhhhhhhhhhhh................hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhh.........hhhhhhhhhh...eeee.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh...............eeee...hhhhhhhhhhhhhhhhhhhhh.......hhhhhh.............hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wds A   4 DSNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLLQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPGIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFACLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNARPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 495
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
   Legend:   → Mismatch (orange background)
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    → 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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYB_SOYBN | P10538)
molecular function
    GO:0016161    beta-amylase activity    Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.
    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.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYB_SOYBN | P10538: 1bfn 1btc 1bya 1byb 1byc 1byd 1q6c 1q6d 1q6e 1q6f 1q6g 1uko 1ukp 1v3h 1v3i 1wdp 1wdq 1wdr

(-) Related Entries Specified in the PDB File

1bfn RECOMBINANT SOYBEAN BETA-AMYLASE COMPLEXED WITH BETA- CYCLODEXTRIN
1byb SOYBEAN BETA-AMYLASE COMPLEXED WITH 200MM MALTOSE AND COMPLEXED WITH MALTOTETRAOSE
1byd SOYBEAN BETA-AMYLASE REACTED WITH 100MM MALTAL AND COMPLEXED WITH D-DEOXYMALTOSE
1q6c SOYBEAN BETA-AMYLASE COMPLEXED WITH MALTOSE
1v3h SOYBEAN BETA-AMYLASE MUTANT (E186Q) COMPLEXED WITH MALTOPENTAOSE
1v3i SOYBEAN BETA-AMYLASE MUTANT (E380Q) COMPLEXED WITH MALTOSE
1wdp THE SAME PROTEIN, WILD TYPE
1wdq THE SAME PROTEIN, MUTANT (T342V)
1wdr THE SAME PROTEIN, MUTANT (T342S)