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(-) Description

Title :  ASPERGILLUS NIGER ATCC9642 ISOPULLULANASE COMPLEXED WITH ISOPANOSE
 
Authors :  M. Mizuno, A. Koide, A. Yamamura, H. Akeboshi, H. Yoshida, S. Kamitori, A. Nishikawa, T. Tonozuka
Date :  05 Sep 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Isopullulanase, Gh49, Dextranase, Pullulan, Beta-Helix, Glycoprotein, Glycosidase, Hydrolase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mizuno, A. Koide, A. Yamamura, H. Akeboshi, H. Yoshida, S. Kamitori Y. Sakano, A. Nishikawa, T. Tonozuka
Crystal Structure Of Aspergillus Niger Isopullulanase, A Member Of Glycoside Hydrolase Family 49
J. Mol. Biol. V. 376 210 2008
PubMed-ID: 18155243  |  Reference-DOI: 10.1016/J.JMB.2007.11.098
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOPULLULANASE
    Chains: A, B
    EC Number: 3.2.1.57
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PHIL-S1
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061
    Strain: ATCC9642

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 29)

Asymmetric Unit (3, 29)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2GLC4Ligand/IonALPHA-D-GLUCOSE
3NAG23Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:24 , PRO A:245 , HOH A:1228 , HOH A:1314 , HOH A:1361BINDING SITE FOR RESIDUE NAG A 1000
02AC2SOFTWAREASN A:25 , SER A:26 , GLN A:27 , ASN A:94 , SER A:164 , GLU A:174 , HOH A:1148 , HOH A:1152 , HOH A:1165 , HOH A:1184 , HOH A:1333 , HOH A:1639 , HOH A:1645BINDING SITE FOR RESIDUE NAG A 1001
03AC3SOFTWARELEU A:54 , ARG A:114 , ASN A:115 , SER A:118 , HOH A:1370 , HOH A:1610 , GLY B:304 , ASN B:305BINDING SITE FOR RESIDUE NAG A 1002
04AC4SOFTWAREASN A:210 , ASP A:230 , HOH A:1082 , HOH A:1117 , HOH A:1222 , HOH A:1362 , HOH A:1540 , HOH A:1631 , ASN B:138 , GLN B:139BINDING SITE FOR RESIDUE NAG A 1003
05AC5SOFTWAREASN A:305 , HOH A:1211 , HOH A:1391 , THR B:40 , GLN B:41 , NAG B:1002BINDING SITE FOR RESIDUE NAG A 1004
06AC6SOFTWAREASN A:381 , HOH A:1392 , SER B:26 , PHE B:184BINDING SITE FOR RESIDUE NAG A 1005
07AC7SOFTWARETYR A:440 , ASN A:448 , THR A:451 , HOH A:1276 , HOH A:1438 , HOH A:1608BINDING SITE FOR RESIDUE NAG A 1006
08AC8SOFTWAREASN A:409 , ASN A:460 , HOH A:1208 , HOH A:1532 , TYR B:147BINDING SITE FOR RESIDUE NAG A 1007
09AC9SOFTWAREASN A:465 , ASN A:491 , HOH A:1245 , HOH A:1311 , HOH A:1463BINDING SITE FOR RESIDUE NAG A 1008
10BC1SOFTWAREALA A:425 , ASN A:503 , HOH A:1354 , HOH A:1357 , HOH B:1249BINDING SITE FOR RESIDUE NAG A 1009
11BC2SOFTWAREASN A:535 , HOH A:1385 , HOH A:1482 , ASN B:120 , SER B:121 , ASN B:122 , TYR B:136 , HOH B:1415BINDING SITE FOR RESIDUE NAG A 1010
12BC3SOFTWAREASN A:453 , ASN A:455 , ASP A:514 , ASN A:516 , ASN A:517 , HOH A:1529BINDING SITE FOR RESIDUE NAG A 1011
13BC4SOFTWAREASN B:24 , PRO B:221 , HOH B:1388BINDING SITE FOR RESIDUE NAG B 1000
14BC5SOFTWAREASP A:372 , VAL A:394 , TRP A:402 , ASN A:428 , PRO A:442 , ASP A:443 , HOH A:1083 , HOH A:1649 , HOH A:1655 , GLC A:2002BINDING SITE FOR RESIDUE GLC A 2001
15BC6SOFTWAREVAL A:394 , GLY A:426 , ASN A:427 , HOH A:1237 , HOH A:1654 , GLC A:2001 , BGC A:2003BINDING SITE FOR RESIDUE GLC A 2002
16BC7SOFTWAREGLN A:88 , TYR A:89 , THR A:90 , GLN A:91 , GLY A:350 , HOH A:1013 , HOH A:1650 , HOH A:1651 , HOH A:1652 , GLC A:2002BINDING SITE FOR RESIDUE BGC A 2003
17BC8SOFTWAREASN B:94 , SER B:164 , GLU B:174 , HOH B:1211 , HOH B:1231 , HOH B:1248 , HOH B:1413 , HOH B:1448BINDING SITE FOR RESIDUE NAG B 1001
18BC9SOFTWARENAG A:1004 , LEU B:54 , ARG B:114 , ASN B:115 , SER B:118 , HOH B:1349BINDING SITE FOR RESIDUE NAG B 1002
19CC1SOFTWAREHIS A:231 , GLU A:254 , PRO A:281 , TYR A:285 , HOH A:1315 , HOH A:1406 , ASN B:138 , HOH B:1220BINDING SITE FOR RESIDUE NAG B 1003
20CC2SOFTWAREGLN A:139 , LEU B:207 , ASN B:210 , ASP B:230 , HOH B:1121 , HOH B:1145 , HOH B:1157 , HOH B:1463BINDING SITE FOR RESIDUE NAG B 1004
21CC3SOFTWAREGLN A:27 , HIS A:106 , HOH A:1633 , ASN B:305 , HOH B:1471BINDING SITE FOR RESIDUE NAG B 1005
22CC4SOFTWAREASN B:381 , HOH B:1434 , HOH B:1440BINDING SITE FOR RESIDUE NAG B 1006
23CC5SOFTWARETYR B:440 , ASN B:448 , THR B:451 , HOH B:1303BINDING SITE FOR RESIDUE NAG B 1007
24CC6SOFTWAREGLY B:452 , ASN B:453 , ASN B:455 , ASP B:514 , ASN B:516 , HOH B:1475BINDING SITE FOR RESIDUE NAG B 1008
25CC7SOFTWAREASN B:409 , ASN B:460 , HOH B:1140 , HOH B:1177 , HOH B:1230 , HOH B:1387BINDING SITE FOR RESIDUE NAG B 1009
26CC8SOFTWAREASN B:465 , LYS B:490 , ASN B:491 , HOH B:1128 , HOH B:1280 , HOH B:1379BINDING SITE FOR RESIDUE NAG B 1010
27CC9SOFTWAREASP B:372 , VAL B:394 , TRP B:402 , ASN B:428 , PRO B:442 , ASP B:443 , HOH B:683 , HOH B:1130 , HOH B:1522 , GLC B:2002BINDING SITE FOR RESIDUE GLC B 2001
28DC1SOFTWAREVAL B:394 , GLY B:426 , ASN B:427 , HOH B:1523 , GLC B:2001 , BGC B:2003BINDING SITE FOR RESIDUE GLC B 2002
29DC2SOFTWAREHOH A:1468 , GLN B:88 , TYR B:89 , THR B:90 , GLN B:91 , GLY B:350 , HOH B:1521 , HOH B:1524 , HOH B:1525 , HOH B:1526 , GLC B:2002BINDING SITE FOR RESIDUE BGC B 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z8G)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:62 -Pro A:63
2Arg A:126 -Pro A:127
3Ala A:166 -Pro A:167
4Thr B:62 -Pro B:63
5Arg B:126 -Pro B:127
6Ala B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z8G)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z8G)

(-) Sequences/Alignments

Asymmetric 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:549
 aligned with IPUA_ASPNG | O00105 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:549
                                    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       505       515       525       535       545       555         
           IPUA_ASPNG    16 VAQAAVTANNSQLLTWWHNTGEINTQTPVADGNVRQSGLYSVKVQTTPASSSLYYDSFVYLAIPGNGMSDQLQYTQGYNQTQAWTSFLYSHDATVKISRNGSSANSNVVIRPTSLNFPVRYDNQSVYITVPYSPTGYRFSVEFDDDLISLAPSGARQPENALLIFASPFENSSTKPQPGSPNSIAPAPGRVLGLNTTSASTVVFNPGVYYFTGHDHMVLSSSVTWVYFAPGAYVKGAVEFLSTASEVKASGHGVLSGEQYVWYADPDEGYQKASGANNNGLRMWRGTLGNSSQTFVLNGVTVSAPPFNSMDWSGNSLDLITCRVDDYKQVGAFYGQTDGLEMYPGTILQDVFYHTDDDGLKMYYSNVTARNIVMWKESVAPVVEFGWTPRNTENVLFDNVDVIHQAYANAGNNPGIFGAVNNYLYAPDGLSSNHSTGNSNMTVRNITWSNFRAEGSSSALFRINPIQNLDNISIKNVSIESFEPLSINTTESWMPVWYDLNNGKQITVTDFSIEGFTVGNTTITASNAASVGRIDGVDPAYAGSVHYID 564
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---2z8gA01 A:19-189 Dex49a from penicillium minioluteum complex, domain 1                                                                                                     -2z8gA02 A:191-564 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee......eee..........eee....eeeeee........eee..eeehhhhhhhhhhhhh.....eeeeeeeee...eeeeee.........eeeehhhhh..eeee..eeeeee......eeeeeee...eeee....eeee.eeeeeeee...............ee....ee..........eeee..eeee......eee.....eeee...eeee..eee.....eeeee...eee...........................eeee.....eeeeee..eee......eeee..hhh.eeeeeeeeeee................eeeeeeeee....ee.....eeeeeeeeee......ee.......eeeeeeeeeeeee....hhhhh...eee..................eeeeeeeeeeeeeeeeeeee...eee...eeeeeeeeeeeeeeee.hhhhh...eee.............eeeeeeeeeee..ee...........eeeehhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8g A  16 REFMAVTANNSQLLTWWHNTGEINTQTPVADGNVRQSGLYSVKVQTTPASSSLYYDSFVYLAIPGNGMSDQLQYTQGYNQTQAWTSFLYSHDATVKISRNGSSANSNVVIRPTSLNFPVRYDNQSVYITVPYSPTGYRFSVEFDDDLISLAPSGARQPENALLIFASPFENSSTKPQPGSPNSIAPAPGRVLGLNTTSASTVVFNPGVYYFTGHDHMVLSSSVTWVYFAPGAYVKGAVEFLSTASEVKASGHGVLSGEQYVWYADPDEGYQKASGANNNGLRMWRGTLGNSSQTFVLNGVTVSAPPFNSMDWSGNSLDLITCRVDDYKQVGAFYGQTDGLEMYPGTILQDVFYHTDDDGLKMYYSNVTARNIVMWKESVAPVVEFGWTPRNTENVLFDNVDVIHQAYANAGNNPGIFGAVNNYLYAPDGLSSNHSTGNSNMTVRNITWSNFRAEGSSSALFRINPIQNLDNISIKNVSIESFEPLSINTTESWMPVWYDLNNGKQITVTDFSIEGFTVGNTTITASNAASVGRIDGVDPAYAGSVHYID 564
                                    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       505       515       525       535       545       555         


Chain B from PDB  Type:PROTEIN  Length:549
 aligned with IPUA_ASPNG | O00105 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:549
                                    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       505       515       525       535       545       555         
           IPUA_ASPNG    16 VAQAAVTANNSQLLTWWHNTGEINTQTPVADGNVRQSGLYSVKVQTTPASSSLYYDSFVYLAIPGNGMSDQLQYTQGYNQTQAWTSFLYSHDATVKISRNGSSANSNVVIRPTSLNFPVRYDNQSVYITVPYSPTGYRFSVEFDDDLISLAPSGARQPENALLIFASPFENSSTKPQPGSPNSIAPAPGRVLGLNTTSASTVVFNPGVYYFTGHDHMVLSSSVTWVYFAPGAYVKGAVEFLSTASEVKASGHGVLSGEQYVWYADPDEGYQKASGANNNGLRMWRGTLGNSSQTFVLNGVTVSAPPFNSMDWSGNSLDLITCRVDDYKQVGAFYGQTDGLEMYPGTILQDVFYHTDDDGLKMYYSNVTARNIVMWKESVAPVVEFGWTPRNTENVLFDNVDVIHQAYANAGNNPGIFGAVNNYLYAPDGLSSNHSTGNSNMTVRNITWSNFRAEGSSSALFRINPIQNLDNISIKNVSIESFEPLSINTTESWMPVWYDLNNGKQITVTDFSIEGFTVGNTTITASNAASVGRIDGVDPAYAGSVHYID 564
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---2z8gB01 B:19-189 Dex49a from penicillium minioluteum complex, domain 1                                                                                                     -2z8gB02 B:191-564 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----Glyco_hydro_49-2z8gB01 B:20-563                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 - Pfam domains (1)
           Pfam domains (2) ----Glyco_hydro_49-2z8gB02 B:20-563                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 - Pfam domains (2)
         Sec.struct. author ............ee......eee..........eee....eeeeee........eee..eeehhhhhhhhhhhhh.....eeeeeeeee...eeeeee.........eeee.......eeee..eeeeee......eeeeeee...eeee....eeee.eeeeeeeee..............ee....ee..........eeee..eeee......eee.....eeee...eeee..eee.....eeeee...eee........hhhhh..............eeee.....eeeeee..eee......eeee..hhh.eeeeeeeeeee................eeeeeeeee....ee.....eeeeeeeeee......ee.......eeeeeeeeeeeee....hhhhh...eee..................eeeeeeeeeeeeeeeeeeee...eee...eeeeeeeeeeeeeeee.hhhhh...eee.............eeeeeeeeeee..ee...........eeee...hhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8g B  16 REFMAVTANNSQLLTWWHNTGEINTQTPVADGNVRQSGLYSVKVQTTPASSSLYYDSFVYLAIPGNGMSDQLQYTQGYNQTQAWTSFLYSHDATVKISRNGSSANSNVVIRPTSLNFPVRYDNQSVYITVPYSPTGYRFSVEFDDDLISLAPSGARQPENALLIFASPFENSSTKPQPGSPNSIAPAPGRVLGLNTTSASTVVFNPGVYYFTGHDHMVLSSSVTWVYFAPGAYVKGAVEFLSTASEVKASGHGVLSGEQYVWYADPDEGYQKASGANNNGLRMWRGTLGNSSQTFVLNGVTVSAPPFNSMDWSGNSLDLITCRVDDYKQVGAFYGQTDGLEMYPGTILQDVFYHTDDDGLKMYYSNVTARNIVMWKESVAPVVEFGWTPRNTENVLFDNVDVIHQAYANAGNNPGIFGAVNNYLYAPDGLSSNHSTGNSNMTVRNITWSNFRAEGSSSALFRINPIQNLDNISIKNVSIESFEPLSINTTESWMPVWYDLNNGKQITVTDFSIEGFTVGNTTITASNAASVGRIDGVDPAYAGSVHYID 564
                                    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       505       515       525       535       545       555
   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  (0, 0)

(no "SCOP Domain" information available for 2Z8G)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Pec_lyase (42)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IPUA_ASPNG | O00105)
molecular function
    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:0051675    isopullulanase activity    Catalysis of the hydrolysis of pullulan to isopanose (6-alpha-maltosylglucose).
biological process
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  2z8g
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  IPUA_ASPNG | O00105
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  3.2.1.57
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  IPUA_ASPNG | O00105
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 Related Entries

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

UniProtKB/Swiss-Prot
        IPUA_ASPNG | O00105: 1wmr 1x0c 3wwg

(-) Related Entries Specified in the PDB File

1wmr CRYSTAL STRUCTURE OF THE SAME PROTEIN AT 2.4 A RESOLUTION WITH DIFFERENT LIGANDS
1x0c CRYSTAL STRUCTURE OF THE SAME PROTEIN WITH DIFFERENT LIGANDS