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(-) Description

Title :  CRYSTAL STRUCTURE OF NEOPULLULANASE E357Q COMPLEX WITH MALTOTETRAOSE
 
Authors :  H. Hondoh, T. Kuriki, Y. Matsuura
Date :  14 Nov 02  (Deposition) - 28 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Barrels, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hondoh, T. Kuriki, Y. Matsuura
Three-Dimensional Structure And Substrate Binding Of Bacillus Stearothermophilus Neopullulanase
J. Mol. Biol. V. 326 177 2003
PubMed-ID: 12547200  |  Reference-DOI: 10.1016/S0022-2836(02)01402-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEOPULLULANASE
    Chains: A, B
    EC Number: 3.2.1.135
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC129
    Expression System Strain: TG-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GLC8Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:207 , MET A:295 , ASP A:468 , ARG A:472 , GLC A:602BINDING SITE FOR RESIDUE GLC A 601
2AC2SOFTWARETYR A:207 , HIS A:247 , PHE A:289 , ARG A:326 , ASP A:328 , VAL A:329 , GLN A:357 , HIS A:423 , ASP A:424 , GLC A:601 , GLC A:603BINDING SITE FOR RESIDUE GLC A 602
3AC3SOFTWAREPHE A:289 , VAL A:329 , GLN A:357 , GLC A:602 , GLC A:604 , TYR B:45BINDING SITE FOR RESIDUE GLC A 603
4AC4SOFTWARETRP A:359 , GLC A:603 , HOH A:1069 , ARG B:83 , ASP B:110 , THR B:111 , ALA B:112BINDING SITE FOR RESIDUE GLC A 604
5AC5SOFTWARETYR B:207 , MET B:295 , ASP B:468 , ARG B:472 , GLC B:606 , HOH B:1241BINDING SITE FOR RESIDUE GLC B 605
6AC6SOFTWARETYR B:207 , HIS B:247 , PHE B:289 , ARG B:326 , ASP B:328 , VAL B:329 , GLN B:357 , HIS B:423 , ASP B:424 , GLC B:605 , GLC B:607BINDING SITE FOR RESIDUE GLC B 606
7AC7SOFTWARETYR A:45 , PHE B:289 , VAL B:329 , GLN B:357 , GLC B:606 , GLC B:608 , HOH B:1232BINDING SITE FOR RESIDUE GLC B 607
8AC8SOFTWAREARG A:83 , THR A:111 , ALA A:112 , HOH A:1008 , TRP B:359 , GLC B:607 , HOH B:1279BINDING SITE FOR RESIDUE GLC B 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J0J)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:276 -Pro A:277
2Glu A:281 -Pro A:282
3Asp A:468 -Pro A:469
4Phe B:276 -Pro B:277
5Asp B:468 -Pro B:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J0J)

(-) Exons   (0, 0)

(no "Exon" information available for 1J0J)

(-) 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:588
 aligned with NEPU_GEOSE | P38940 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:588
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580        
           NEPU_GEOSE     1 MRKEAIYHRPADNFAYAYDSETLHLRLRTKKDDIDRVELLHGDPYDWQNGAWQFQMMPMRKTGSDELFDYWFAEVKPPYRRLRYGFVLYSGEEKLVYTEKGFYFEVPTDDTAYYFCFPFLHRVDLFEAPDWVKDTVWYQIFPERFANGNPSISPEGSRPWGSEDPTPTSFFGGDLQGIIDHLDYLVDLGITGIYLTPIFRSPSNHKYDTADYFEVDPHFGDKETLKTLIDRCHEKGIRVMLDAVFNHCGYEFAPFQDVWKNGESSKYKDWFHIHEFPLQTEPRPNYDTFRFVPQMPKLNTANPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHEFWREFRQEVKALKPDVYILGEIWHDAMPWLRGDQFDAVMNYPFTDGVLRFFAKEEISARQFANQMMHVLHSYPNNVNEAAFNLLGSHDTSRILTVCGGDIRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPMQQNKELHQHVKQLIALRKQYRSLRRGEISFLHADDEMNYLIYKKTDGDETVLVIINRSDQKADIPIPLDARGTWLVNLLTGERFAAEAETLCTSLPPYGFVLYAIEHW 588
               SCOP domains d1j0ja1 A:1-123 Neopullulanase, N-terminal domain                                                                          d1j0ja3 A:124-505 Neopullulanase, central domain                                                                                                                                                                                                                                                                                                                                              d1j0ja2 A:506-588 Neopullulanase                                                    SCOP domains
               CATH domains 1j0jA01 A:1-125 Immunoglobulins                                                                                              1j0jA02 A:126-245,A:300-505 Glycosidases                                                                                ------------------------------------------------------1j0jA02 A:126-245,A:300-505 Glycosidases                                                                                                                                                                      1j0jA04 A:506-588 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh........eeeee..eeeeeeeee.....eeeeeee....ee..ee..eeeeeeeeee...eeeeeeee......eeeeeeeee..eeeeee..eee...........eee...hhhhh...hhhhhhh.eeeehhhhh............................hhhhhhhhhhhhhhhh..eeee...ee..........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhhh..............................hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh............hhhhhh..hhhhhhhhhhhhhhh....eee.hhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee.......eeeeeee.....eeeeee.....eeee.......eeeee.....eee......eeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j0j A   1 MRKEAIYHRPADNFAYAYDSETLHLRLRTKKDDIDRVELLHGDPYDWQNGAWQFQMMPMRKTGSDELFDYWFAEVKPPYRRLRYGFVLYSGEEKLVYTEKGFYFEVPTDDTAYYFCFPFLHRVDLFEAPDWVKDTVWYQIFPERFANGNPSISPEGSRPWGSEDPTPTSFFGGDLQGIIDHLDYLVDLGITGIYLTPIFRSPSNHKYDTADYFEVDPHFGDKETLKTLIDRCHEKGIRVMLDAVFNHCGYEFAPFQDVWKNGESSKYKDWFHIHEFPLQTEPRPNYDTFAFVPQMPKLNTANPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHEFWREFRQEVKALKPDVYILGQIWHDAMPWLRGDQFDAVMNYPFTDGVLRFFAKEEISARQFANQMMHVLHSYPNNVNEAAFNLLGSHDTSRILTVCGGDIRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPMQQNKELHQHVKQLIALRKQYRSLRRGEISFLHADDEMNYLIYKKTDGDETVLVIINRSDQKADIPIPLDARGTWLVNLLTGERFAAEAETLCTSLPPYGFVLYAIEHW 588
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580        


Chain B from PDB  Type:PROTEIN  Length:588
 aligned with NEPU_GEOSE | P38940 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:588
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580        
           NEPU_GEOSE     1 MRKEAIYHRPADNFAYAYDSETLHLRLRTKKDDIDRVELLHGDPYDWQNGAWQFQMMPMRKTGSDELFDYWFAEVKPPYRRLRYGFVLYSGEEKLVYTEKGFYFEVPTDDTAYYFCFPFLHRVDLFEAPDWVKDTVWYQIFPERFANGNPSISPEGSRPWGSEDPTPTSFFGGDLQGIIDHLDYLVDLGITGIYLTPIFRSPSNHKYDTADYFEVDPHFGDKETLKTLIDRCHEKGIRVMLDAVFNHCGYEFAPFQDVWKNGESSKYKDWFHIHEFPLQTEPRPNYDTFRFVPQMPKLNTANPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHEFWREFRQEVKALKPDVYILGEIWHDAMPWLRGDQFDAVMNYPFTDGVLRFFAKEEISARQFANQMMHVLHSYPNNVNEAAFNLLGSHDTSRILTVCGGDIRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPMQQNKELHQHVKQLIALRKQYRSLRRGEISFLHADDEMNYLIYKKTDGDETVLVIINRSDQKADIPIPLDARGTWLVNLLTGERFAAEAETLCTSLPPYGFVLYAIEHW 588
               SCOP domains d1j0jb1 B:1-123 Neopullulanase, N-terminal domain                                                                          d1j0jb3 B:124-505 Neopullulanase, central domain                                                                                                                                                                                                                                                                                                                                              d1j0jb2 B:506-588 Neopullulanase                                                    SCOP domains
               CATH domains 1j0jB01 B:1-125 Immunoglobulins                                                                                              1j0jB02 B:126-245,B:300-505 Glycosidases                                                                                ------------------------------------------------------1j0jB02 B:126-245,B:300-505 Glycosidases                                                                                                                                                                      1j0jB04 B:506-588 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....hhh.eee.....eeeeeeee.....eeeeeee............eeeeeeeeee...eeeeeeee......eeeeeeee......eee..eee......hhhhheee...hhhhh...hhhhhhh.eeeehhhhh...hhhhh....................hhhhhhhhhhhhhhhh..eeee...ee..........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhhh................ee..eeeee.....hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee............hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhheeee........eeeeeee....eeeeeee.....eeee.......eeeee.....eee......eeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j0j B   1 MRKEAIYHRPADNFAYAYDSETLHLRLRTKKDDIDRVELLHGDPYDWQNGAWQFQMMPMRKTGSDELFDYWFAEVKPPYRRLRYGFVLYSGEEKLVYTEKGFYFEVPTDDTAYYFCFPFLHRVDLFEAPDWVKDTVWYQIFPERFANGNPSISPEGSRPWGSEDPTPTSFFGGDLQGIIDHLDYLVDLGITGIYLTPIFRSPSNHKYDTADYFEVDPHFGDKETLKTLIDRCHEKGIRVMLDAVFNHCGYEFAPFQDVWKNGESSKYKDWFHIHEFPLQTEPRPNYDTFAFVPQMPKLNTANPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHEFWREFRQEVKALKPDVYILGQIWHDAMPWLRGDQFDAVMNYPFTDGVLRFFAKEEISARQFANQMMHVLHSYPNNVNEAAFNLLGSHDTSRILTVCGGDIRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPMQQNKELHQHVKQLIALRKQYRSLRRGEISFLHADDEMNYLIYKKTDGDETVLVIINRSDQKADIPIPLDARGTWLVNLLTGERFAAEAETLCTSLPPYGFVLYAIEHW 588
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J0J)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NEPU_GEOSE | P38940)
molecular function
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031216    neopullulanase activity    Catalysis of the hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
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/Swiss-Prot
        NEPU_GEOSE | P38940: 1j0h 1j0i 1j0k

(-) Related Entries Specified in the PDB File

1j0h 1J0H CONTAINS CHLORIDE ION AND CALCIUM ION
1j0i IJ0I CONTAINS PANOSE
1j0k 1J0K CONTAINS ISOPANOSE AND E357Q MUTANT