Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SOYBEAN BETA-AMYLASE MUTANT (E178Y) WITH INCREASED PH OPTIMUM AT PH 7.1
 
Authors :  A. Hirata, M. Adachi, A. Sekine, Y. N. Kang, S. Utsumi, B. Mikami
Date :  13 Aug 03  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Barrels, Beta-Amylase, Maltose Complex, Increased Ph Optimum, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hirata, M. Adachi, A. Sekine, Y. N. Kang, S. Utsumi, B. Mikami
Structural And Enzymatic Analysis Of Soybean {Beta}-Amylase Mutants With Increased Ph Optimum
J. Biol. Chem. V. 279 7287 2004
PubMed-ID: 14638688  |  Reference-DOI: 10.1074/JBC.M309411200
(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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:20 , ASP A:53 , TRP A:55 , HIS A:93 , ASP A:101 , ARG A:420 , BGC A:497 , HOH A:593 , HOH A:594 , HOH A:599 , GLC A:1497BINDING SITE FOR RESIDUE BGC A 496
2AC2SOFTWAREALA A:184 , LYS A:295 , THR A:342 , GLU A:380 , ASN A:381 , ALA A:382 , LEU A:419 , BGC A:496 , GLC A:498 , HOH A:500 , HOH A:581 , HOH A:594BINDING SITE FOR RESIDUE BGC A 497
3AC3SOFTWAREVAL A:99 , ALA A:184 , GLU A:186 , LYS A:295 , THR A:342 , GLU A:380 , ALA A:382 , BGC A:496 , GLC A:498 , HOH A:500 , HOH A:581 , HOH A:594BINDING SITE FOR RESIDUE GLC A 1497
4AC4SOFTWAREGLU A:186 , ARG A:188 , TYR A:192 , TRP A:198 , PHE A:200 , SER A:297 , GLY A:298 , HIS A:300 , TRP A:301 , THR A:342 , CYS A:343 , MET A:346 , BGC A:497 , BGC A:499 , HOH A:596 , GLC A:1497BINDING SITE FOR RESIDUE GLC A 498
5AC5SOFTWAREVAL A:99 , GLN A:194 , HIS A:300 , MET A:346 , LEU A:383 , GLC A:498 , HOH A:596BINDING SITE FOR RESIDUE BGC A 499
6AC6SOFTWAREGLN A:77 , ARG A:372 , THR A:480 , LEU A:481BINDING SITE FOR RESIDUE SO4 A 900
7AC7SOFTWAREHIS A:146 , ARG A:326 , ARG A:372 , LYS A:478BINDING SITE FOR RESIDUE SO4 A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q6F)

(-) 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 1Q6F)

(-) 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 1Q6F)

(-) 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:490
 aligned with AMYB_SOYBN | P10538 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:490
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496
           AMYB_SOYBN     7 NMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLFQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPRIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNAKPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 496
               SCOP domains d1q6fa_ A: beta-Amylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1q6fA00 A:6-495 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------Glyco_hydro_14-1q6fA01 A:15-437                                                                                                                                                                                                                                                                                                                                                                                                        ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeee.............hhhhhhhhhhhhhhhh..eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhh...eee.....eeeeee.hhhh........hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhh......hhhhh............hhhhhhhhhhhhhhh................hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhh.........hhhhhhhhhhh..eeee.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh...............eeee...hhhhhhhhhhhhhhhhhhhhh.......hhhhhh.............hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q6f A   6 NMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLLQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIYVGLGPAGELRYPSYPQSQGWEFPGIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNARPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 495
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
   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  (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:419 - Arg A:420   [ RasMol ]  
    Phe A:200 - Pro A:201   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1q6f
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AMYB_SOYBN | P10538
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AMYB_SOYBN | P10538
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 1q6g 1uko 1ukp 1v3h 1v3i 1wdp 1wdq 1wdr 1wds

(-) Related Entries Specified in the PDB File

1q6c THE SAME PROTEIN COMPLEXED WITH MALTOSE
1q6d THE SAME PROTEIN, M51T MUTANT
1q6e THE SAME PROTEIN, E178Y MUTANT AT PH 5.4
1q6g THE SAME PROTEIN, N340T MUTANT