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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF KLEBSIELLA PNEUMONIAE PULLULANASE COMPLEXED WITH ISOMALTOSE
 
Authors :  B. Mikami, H. Iwamoto, Y. Katsuya, H. -J. Yoon, E. Demirkan-Sarikaya, D. Malle
Date :  23 Dec 05  (Deposition) - 13 Jun 06  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Multiple Domain, Beta-Alpha-Barrel, Alpha-Amylase-Family, Complex With Isomaltose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Mikami, H. Iwamoto, D. Malle, H. -J. Yoon, E. Demirkan-Sarikaya, Y. Mezaki, Y. Katsuya
Crystal Structure Of Pullulanase: Evidence For Parallel Binding Of Oligosaccharides In The Active Site
J. Mol. Biol. V. 359 690 2006
PubMed-ID: 16650854  |  Reference-DOI: 10.1016/J.JMB.2006.03.058
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PULLULANASE
    Chains: A
    EC Number: 3.2.1.41
    Mutation: YES
    Organism Scientific: KLEBSIELLA AEROGENES
    Organism Taxid: 28451
    Strain: W70

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA4Ligand/IonCALCIUM ION
3GLC1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:557 , ASP A:560 , ASP A:890 , TYR A:892 , BGC A:1098 , HOH A:1139 , HOH A:1241 , HOH A:1433 , HOH A:2351BINDING SITE FOR RESIDUE GLC A 1097
2AC2SOFTWARETHR A:642 , LEU A:678 , ASP A:834 , GLC A:1097 , HOH A:1505 , HOH A:2351 , HOH A:2384BINDING SITE FOR RESIDUE BGC A 1098
3AC3SOFTWAREALA A:550 , ASP A:553 , TYR A:555 , ASP A:893 , HOH A:1272 , HOH A:1494 , HOH A:1495BINDING SITE FOR RESIDUE CA A 2401
4AC4SOFTWAREASP A:994 , SER A:1001 , ASP A:1003 , VAL A:1006 , GLN A:1070 , HOH A:1525BINDING SITE FOR RESIDUE CA A 2402
5AC5SOFTWAREHOH A:1247 , HOH A:1253 , HOH A:1425 , HOH A:1746 , HOH A:1747 , HOH A:1748BINDING SITE FOR RESIDUE CA A 2403
6AC6SOFTWAREASP A:481 , LEU A:482 , GLU A:487 , GLU A:568 , HOH A:1254 , HOH A:1496BINDING SITE FOR RESIDUE CA A 2404

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:503 -A:518
2A:643 -A:644

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FH8)

(-) Exons   (0, 0)

(no "Exon" information available for 2FH8)

(-) 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:922
 aligned with PULA_ENTAE | P07811 from UniProtKB/Swiss-Prot  Length:1096

    Alignment length:1056
                                                                                                                                                                                                                                                                     285                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                   284 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1016  1017                                                                      1091 1092    
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280   | | 289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      |  -  |   1024      1034      1044      1054      1064      1074      1084      |  - |    
          PULA_ENTAE     51 DVVVRLPDVAVPGEAVQASARQAVIHLVDIAGITSSTPADYATKNLYLWNNETCDALSAPVADWNDVSTTPTGSDKYGPYWVIPLTKESGSINVIVRDGTNKLIDSGRVSFSDFTDRTVSVIAGNSAVYDSRADAFRAAFGVALADAHWVDKTTLLWPGGENKPIVRLYYSHSSKVAADSNGEFSDKYVKLTPTTVNQQVSMRFPHLASYPAFKLPDDVNVDELLQGDDGGIAE-SDGILSLSHPGADRRRAGRYLCRRAEALSYGAQLTDSGVTFRVWAPTAQQVELVIYSADKKVIASHPMTRDSASGAWSWQGGSDLKGAFYRYAMTVYHPQSRKVEQYEVTDPYAHSLSTNSEYSQVVDLNDSALKPEGWDGLTMPHAQKTKADLAKMTIHESHIRDLSAWDQTVPAELRGKYLALTAQESNMVQHLKQLSASGVTHIELLPVFDLATVNEFSDKVADIQQPFSRLCEVNSAVKSSEFAGYCDSGSTVEEVLTQLKQNDSKDNPQVQALNTLVAQTDSYNWGYDPFHYTVPEGSYATDPEGTARIKEFRTMIQAIKQDLGMNVIMDVVYNHTNAAGPTDRTSVLDKIVPWYYQRLNETTGSVESATCCSDSAPEHRMFAKLIADSLAVWTTDYKIDGFRFDLMGYHPKAQILSAWERIKALNPDIYFFGEGWDSNQSDRFEIASQINLKGTGIGTFSDRLRDAVRGGGPFDSGDALRQNQGVGSGAGVLPNELTTLSDDQARHLADLTRLGMAGNLADFVLIDKDGAVKRGSEIDYNGAPGGYAADPTEVVNYVSKHDNQTLWDMISYKAAQEADLDTRVRMQAVSLATVMLGQGIAFDQQGSELLRSKSFTRDSYDSGDWFNRVDYSLQDNNYNVGMPRSSDDGSNYDIIARVKDAVATPGETELKQMTAFYQELTALRKSSPLFTLGDGATVMKRVDFRNTGADQQTGLLVMTIDDGMQAG-----RQSGQPCRRHRGGDQRRAGKPDAAGLRRHIAPAERYSAGGGRPVAGERVQVAADGSVTLPAWSVAVLELPQASRR----ALACR 1096
               SCOP domains -----------------------------------------------------------------------------------------------------------------------------------------d2fh8a1 A:170-287 Pullulanase PulA                                                                                    d2fh8a2 A:288-402 Pullulanase PulA                                                                                 d2fh8a3 A:403-965 Pullulanase PulA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 d2fh8a4 A:966-1083 Pullulanase PulA                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........---------------------------------------------------------------------------------------------------------------------------------.........eeeee..eee.hhhh...eeeeeee...............eeee.eee..hhhhhhhhhhhh...eee.....hhhhhh..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhh...eeee....eeeeee...eeeeeeeee.....eeeeee.ee.....eeeeeehhhhh..eeeeeeeeee....eeeeeee........hhhhh.ee.....hhhhh..hhhhh.......hhhhhhh.eeeeehhhhhhh.....hhhhh.hhhhhhh..hhhhhhhhhhhhh...eeee...eee.....hhhhh.....hhhhhhhhhhhhhh..hhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhh.......eeeeeee..........hhhhhhhhhhhhhhhhh...eeeeee...ee..........hhhhhh....................ee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee........................eee.hhhhhhhhh.......hhhhhh.hhhhh...........hhhhhhhhhhhhhhhhh......eee.....eee....ee..ee.....hhh.eee........hhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeeee.hhhhh...........hhhhhhh...............hhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhheeee.........eeeeeee.hhhhh......eeeeeeeee.....e--ee........eehhhh--hhhhhhh....-.ee.....eee...eeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2fh8 A   32 DVVVRLPD---------------------------------------------------------------------------------------------------------------------------------AAFGVALADAHWVDKTTLLWPGGENKPIVRLYYSHSSKVAADSNGEFSDKYVKLTPTTVNQQVSMRFPHLASYPAFKLPDDVNVDELLQGETVAIAAESDGILSSATQVQTAGVLDDTYAAAAEALSYGAQLTDSGVTFRVWAPTAQQVELVIYSADKKVIASHPMTRDSASGAWSWQGGSDLKGAFYRYAMTVYHPQSRKVEQYEVTDPYAHSLSTNSEYSQVVDLNDSALKPEGWDGLTMPHAQKTKADLAKMTIHESHIRDLSAWDQTVPAELRGKYLALTAQESNMVQHLKQLSASGVTHIELLPVFDLATVNEFSDKVADIQQPFSRLCEVNSAVKSSEFAGYCDSGSTVEEVLTQLKQNDSKDNPQVQALNTLVAQTDSYNWGYDPFHYTVPEGSYATDPEGTARIKEFRTMIQAIKQDLGMNVIMDVVYNHTNAAGPTDRTSVLDKIVPWYYQRLNETTGSVESATCCSDSAPEHRMFAKLIADSLAVWTTDYKIDGFRFDLMLYHPKAQILSAWERIKALNPDIYFFGEGWDSNQSDRFEIASQINLKGTGIGTFSDRLRDAVRGGGPFDSGDALRQNQGVGSGAGVLPNELTTLSDDQARHLADLTRLGMAGNLADFVLIDKDGAVKRGSEIDYNGAPGGYAADPTEVVNYVSKHDNQTLWDMISYKAAQEADLDTRVRMQAVSLATVMLGQGIAFDQQGSELLRSKSFTRDSYDSGDWFNRVDYSLQDNNYNVGMPRSSDDGSNYDIIARVKDAVATPGETELKQMTAFYQELTALRKSSPLFTLGDGATVMKRVDFRNTGADQQTGLLVMTIDDGMQAGASLDSRVDGIVVAINAAPESR--TLQDFAGTSLQLSAIQ--QAAGDRSLASG-VQVAADGSVTLPAWSVAVLELPQGESQGAGLPVSSK 1083
                                   | -         -         -         -         -         -         -         -         -         -         -         -         -       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       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012       | -|     1030     |1038        |-|     1057      1067      1077      
                                  39                                                                                                                               170                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              1020  |           1036  |      1047 |                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1021              1037        1048
   Legend:   → Mismatch (orange background)
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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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FH8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FH8)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PULA_ENTAE | P07811)
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.
    GO:0051060    pullulanase activity    Catalysis of the hydrolysis of (1,6)-alpha-D-glucosidic linkages in pullulan (a linear polymer of alpha-(1,6)-linked maltotriose units) and in amylopectin and glycogen, and the a- and b-limit dextrins of amylopectin and glycogen.
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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  2fh8
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  PULA_ENTAE | P07811
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  3.2.1.41
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 Related Entries

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

UniProtKB/Swiss-Prot
        PULA_ENTAE | P07811: 2fgz 2fh6 2fhb 2fhc 2fhf

(-) Related Entries Specified in the PDB File

2fgz APO PULLULANASE
2fh6 PULLULANASE COMPLEXED WITH GLUCOSE
2fhb PULLULANASE COMPLEXED WITH MALTOSE
2fhc PULLULANASE COMPLEXED WITH MALTOTRIOSE
2fhf PULLULANASE COMPLEXED WITH MALTOTETRAOSE