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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) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
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
(for further references see the PDB file header)

(-) 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  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MAL2Ligand/IonMALTOSE
2SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:53 , TRP A:55 , HIS A:93 , VAL A:99 , ASP A:101 , ALA A:184 , GLU A:186 , LYS A:295 , VAL A:342 , GLU A:380 , ASN A:381 , ALA A:382 , LEU A:419 , ARG A:420 , MAL A:498 , HOH A:511 , HOH A:512 , HOH A:521 , HOH A:555 , HOH A:596BINDING SITE FOR RESIDUE MAL A 496
2AC2SOFTWAREVAL A:99 , GLU A:186 , ARG A:188 , TYR A:192 , TRP A:198 , PHE A:200 , SER A:297 , GLY A:298 , HIS A:300 , VAL A:342 , CYS A:343 , MET A:346 , LEU A:383 , MAL A:496 , HOH A:552 , HOH A:805BINDING SITE FOR RESIDUE MAL A 498
3AC3SOFTWAREHIS A:146 , ARG A:326 , ARG A:330 , ARG A:372 , HOH A:867 , HOH A:958 , HOH A:977 , HOH A:1073 , HOH A:1138 , HOH A:1288BINDING SITE FOR RESIDUE SO4 A 2000
4AC4SOFTWAREGLN A:77 , ARG A:372 , THR A:480 , LEU A:481 , HOH A:700 , HOH A:774 , HOH A:848 , HOH A:1069BINDING SITE FOR RESIDUE SO4 A 2001
5AC5SOFTWAREHIS A:119 , ARG A:130 , HOH A:860 , HOH A:1025 , HOH A:1211BINDING SITE FOR RESIDUE SO4 A 2002
6AC6SOFTWAREARG A:347 , SER A:349 , LYS A:428 , HOH A:746 , HOH A:800 , HOH A:1150BINDING SITE FOR RESIDUE SO4 A 2003
7AC7SOFTWARELYS A:356 , LYS A:453 , HOH A:715 , HOH A:1035 , HOH A:1148BINDING SITE FOR RESIDUE SO4 A 2004

(-) SS Bonds  (0, 0)

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

(-) 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 1WDQ)

(-) 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 1WDQ)

(-) 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:493
 aligned with AMYB_SOYBN | P10538 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:493
                                    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   
           AMYB_SOYBN     4 SDSNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLFQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPRIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNAKPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 496
               SCOP domains --d1wdqa1 A:5-495 beta-Amylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1wdqA00 A:3-495 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------Glyco_hydro_14-1wdqA01 A:15-437                                                                                                                                                                                                                                                                                                                                                                                                        ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....eeee.............hhhhhhhhhhhhhhh...eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhh...eee.....eeeeee.hhhh........hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhh......hhhhh............hhhhhhhhhhhhhhh................hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhh.........hhhhhhhhhh...eeee.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh...............eeee...hhhhhhhhhhhhhhhhhhhhh.......hhhhhh.............hhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wdq A   3 SDSNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLLQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPGIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFVCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNARPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 495
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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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  1wdq
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  3.2.1.2
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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 1wdr 1wds

(-) 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
1wdr THE SAME PROTEIN, MUTANT (T342S)
1wds THE SAME PROTEIN, MUTANT (T342A)