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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF KLEBSIELLA PNEUMONIAE PULLULANASE COMPLEXED WITH MALTOTRIOSE
 
Authors :  B. Mikami, H. Iwamoto, Y. Katsuya, H. -J. Yoon, E. Demirkan-Sarikaya, D. Malle
Date :  23 Dec 05  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Multiple Domain, Beta-Alpha-Barrel, Alpha-Amylase-Family, Complex With Maltotriose, 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  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2GLC8Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:68 , THR A:642 , ARG A:889 , ASP A:890 , GLC A:1093 , GLC A:1097 , GLC A:1098 , HOH A:1266 , HOH A:1675BINDING SITE FOR RESIDUE GLC A 1092
02AC2SOFTWARESER A:67 , GLU A:706 , TRP A:708 , ASP A:834 , ASN A:835 , GLC A:1092 , GLC A:1094 , GLC A:1098 , HOH A:1675BINDING SITE FOR RESIDUE GLC A 1093
03AC3SOFTWARESER A:66 , SER A:67 , ASP A:734 , ARG A:737 , PHE A:746 , GLC A:1093 , HOH A:1607 , HOH A:1615 , HOH A:1719 , HOH A:1960BINDING SITE FOR RESIDUE GLC A 1094
04AC4SOFTWARECYS A:643 , TYR A:892 , GLC A:1097 , HOH A:2252BINDING SITE FOR RESIDUE GLC A 1096
05AC5SOFTWARETRP A:557 , TYR A:559 , ASP A:560 , ASP A:890 , TYR A:892 , GLC A:1092 , GLC A:1096 , GLC A:1098 , HOH A:1139 , HOH A:1241BINDING SITE FOR RESIDUE GLC A 1097
06AC6SOFTWARETRP A:557 , TYR A:559 , HIS A:607 , THR A:642 , ARG A:675 , ASP A:677 , LEU A:678 , GLU A:706 , HIS A:833 , ASP A:834 , GLC A:1092 , GLC A:1093 , GLC A:1097BINDING SITE FOR RESIDUE GLC A 1098
07AC7SOFTWARETYR A:78 , ASP A:138 , GLC A:1100BINDING SITE FOR RESIDUE GLC A 1099
08AC8SOFTWARETYR A:78 , TRP A:95 , LYS A:133 , GLC A:1099 , HOH A:2348BINDING SITE FOR RESIDUE GLC A 1100
09AC9SOFTWAREALA 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
10BC1SOFTWAREASP A:994 , SER A:1001 , ASP A:1003 , VAL A:1006 , GLN A:1070 , HOH A:1525BINDING SITE FOR RESIDUE CA A 2402
11BC2SOFTWAREHOH A:1247 , HOH A:1253 , HOH A:1425 , HOH A:1746 , HOH A:1747 , HOH A:1748BINDING SITE FOR RESIDUE CA A 2403
12BC3SOFTWAREASP A:481 , LEU A:482 , GLU A:487 , GLU A:568 , HOH A:1254 , HOH A:1496BINDING SITE FOR RESIDUE CA A 2404
13BC4SOFTWAREASP A:148 , THR A:150 , ASP A:162BINDING SITE FOR RESIDUE CA A 2405

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:85 -A:122
2A:503 -A:518
3A:643 -A:644

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FHC)

(-) 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:1052
 aligned with PULA_ENTAE | P07811 from UniProtKB/Swiss-Prot  Length:1096

    Alignment length:1057
                                                                                                                                      158                                                                                                                             285                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                    157 |                                                                                                                           284 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1016  1017                                                                      1091 1092    
                                    60        70        80        90       100       110       120       130       140       150      |159       169       179       189       199       209       219       229       239       249       259       269       279    | |288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008       | -   |  1023      1033      1043      1053      1063      1073      1083       | -  |    
          PULA_ENTAE     51 DVVVRLPDVAVPGEAVQASARQAVIHLVDIAGITSSTPADYATKNLYLWNNETCDALSAPVADWNDVSTTPTGSDKYGPYWVIPLTKESGSINVIVRDGTNKLIDSG-RVSFSDFTDRTVSVIAGNSAVYDSRADAFRAAFGVALADAHWVDKTTLLWPGGENKPIVRLYYSHSSKVAADSNGEFSDKYVKLTPTTVNQQVSMRFPHLASYPAFKLPDDVNVDELLQGDDGGIAE-SDGILSLSHPGADRRRAGRYLCRRAEALSYGAQLTDSGVTFRVWAPTAQQVELVIYSADKKVIASHPMTRDSASGAWSWQGGSDLKGAFYRYAMTVYHPQSRKVEQYEVTDPYAHSLSTNSEYSQVVDLNDSALKPEGWDGLTMPHAQKTKADLAKMTIHESHIRDLSAWDQTVPAELRGKYLALTAQESNMVQHLKQLSASGVTHIELLPVFDLATVNEFSDKVADIQQPFSRLCEVNSAVKSSEFAGYCDSGSTVEEVLTQLKQNDSKDNPQVQALNTLVAQTDSYNWGYDPFHYTVPEGSYATDPEGTARIKEFRTMIQAIKQDLGMNVIMDVVYNHTNAAGPTDRTSVLDKIVPWYYQRLNETTGSVESATCCSDSAPEHRMFAKLIADSLAVWTTDYKIDGFRFDLMGYHPKAQILSAWERIKALNPDIYFFGEGWDSNQSDRFEIASQINLKGTGIGTFSDRLRDAVRGGGPFDSGDALRQNQGVGSGAGVLPNELTTLSDDQARHLADLTRLGMAGNLADFVLIDKDGAVKRGSEIDYNGAPGGYAADPTEVVNYVSKHDNQTLWDMISYKAAQEADLDTRVRMQAVSLATVMLGQGIAFDQQGSELLRSKSFTRDSYDSGDWFNRVDYSLQDNNYNVGMPRSSDDGSNYDIIARVKDAVATPGETELKQMTAFYQELTALRKSSPLFTLGDGATVMKRVDFRNTGADQQTGLLVMTIDDGMQAG-----RQSGQPCRRHRGGDQRRAGKPDAAGLRRHIAPAERYSAGGGRPVAGERVQVAADGSVTLPAWSVAVLELPQASRR----ALACR 1096
               SCOP domains d2fhca3 A:32-162 Pullulanase PulA                                                                                                  d2fhca2 A:163-287 Pullulanase PulA                                                                                           d2fhca1 A:288-402 Pullulanase PulA                                                                                 d2fhca5 A:403-965 Pullulanase PulA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 d2fhca4 A:966-1083 Pullulanase PulA                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee.hhhhhh...........eeee.......................eee..eeeeeee......eeeeeeee..ee......eee.......eeee.........hhhhhhhhh.......eeeee..eee.hhhh...eeeeeee................eee.eee..hhhhhhhhhhhh...eee.....hhhhhh..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhh...eeee....eeeeee.....eeeeeee.....eeeeee.ee.....eeeeeehhhhh..eeeeeeeeee....eeeeeee........hhhhh.ee.....hhhhh..hhhhh.......hhhhhhh.eeeeehhhhhhh.....hhhhh.hhhhhhh..hhhhhhhhhhhhhh..eeee...eee.....hhhhh.....hhhhhhhhhhhhhh..hhhhh....hhhhhhhhhh.......hhhhhhhhhhh..........eeeeeee..........hhhhhhhhhhhhhhhhh...eeeeee...ee..........hhhhhh....................ee....hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh.....eeee........................eee.hhhhhhhhh.......hhhhhh.hhhhh...........hhhhhhhhhhhhhhhhh......eee.....eee....ee..ee.....hhh.eee........hhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeeee.hhhhh...........hhhhhhh...............hhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhheeee.........eeeeeee............eeeeeeeee.....e--ee........eehhhh--hhhhhhh....-.ee.....eee...eeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fhc A   32 DVVVRLPDVAVPGEAVQASARQAVIHLVDIAGITSSTPADYATKNLYLWNNETCDALSAPVADWNDVSTTPTGSDKYGPYWVIPLTKESGCINVIVRDGTNKLIDSDLRVSFSDFTDRTVSVIAGNSAVYDSRADAFRAAFGVALADAHWVDKTTLLWPGGENKPIVRLYYSHSSKVAADSNGEFSDKYVKLTPTTVNQQVSMRFPHLASYPAFKLPDDVNVDELLQGETVAIAAESDGILSSATQVQTAGVLDDTYAAAAEALSYGAQLTDSGVTFRVWAPTAQQVELVIYSADKKVIASHPMTRDSASGAWSWQGGSDLKGAFYRYAMTVYHPQSRKVEQYEVTDPYAHSLSTNSEYSQVVDLNDSALKPEGWDGLTMPHAQKTKADLAKMTIHESHIRDLSAWDQTVPAELRGKYLALTAQESNMVQHLKQLSASGVTHIELLPVFDLATVNEFSDKVADIQQPFSRLCEVNSAVKSSEFAGYCDSGSTVEEVLTQLKQNDSKDNPQVQALNTLVAQTDSYNWGYDPFHYTVPEGSYATDPEGTARIKEFRTMIQAIKQDLGMNVIMDVVYNHTNAAGPTDRTSVLDKIVPWYYQRLNETTGSVESATCCSDSAPEHRMFAKLIADSLAVWTTDYKIDGFRFDLMLYHPKAQILSAWERIKALNPDIYFFGEGWDSNQSDRFEIASQINLKGTGIGTFSDRLRDAVRGGGPFDSGDALRQNQGVGSGAGVLPNELTTLSDDQARHLADLTRLGMAGNLADFVLIDKDGAVKRGSEIDYNGAPGGYAADPTEVVNYVSKHDNQTLWDMISYKAAQEADLDTRVRMQAVSLATVMLGQGIAFDQQGSELLRSKSFTRDSYDSGDWFNRVDYSLQDNNYNVGMPRSSDDGSNYDIIARVKDAVATPGETELKQMTAFYQELTALRKSSPLFTLGDGATVMKRVDFRNTGADQQTGLLVMTIDDGMQAGASLDSRVDGIVVAINAAPESR--TLQDFAGTSLQLSAIQ--QAAGDRSLASG-VQVAADGSVTLPAWSVAVLELPQGESQGAGLPVSSK 1083
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011        |- |    1029      1037      1047 |    1056      1066      1076       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     1020  |           1036  |      1047 |                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        1021              1037        1048
   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  (4, 5)

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 2FHC)

(-) Pfam Domains  (0, 0)

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

(-) 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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  2fhc
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 Related Entries

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

UniProtKB/Swiss-Prot
        PULA_ENTAE | P07811: 2fgz 2fh6 2fh8 2fhb 2fhf

(-) Related Entries Specified in the PDB File

2fgz APO PULLULANASE
2fh6 PULLULANASE COMPLEXED WITH GLUCOSE
2fh8 PULLULANASE COMPLEXED WITH ISOMALTOSE
2fhb PULLULANASE COMPLEXED WITH MALTOSE
2fhf PULLULANASE COMPLEXED WITH MALTOTETRAOSE