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(-) Description

Title :  CRYSTAL STRUCTURE OF FERULOYL ESTERASE B FROM ASPERGILLUS ORYZAE
 
Authors :  K. Suzuki, T. Ishida, K. Igarashi, T. Koseki, S. Fushinobu
Date :  25 Nov 13  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta-Hydrolase Fold, Hydrolase, Glycosylation, Extracellular (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Suzuki, A. Hori, K. Kawamoto, R. R. Thangudu, T. Ishida, K. Igarashi M. Samejima, T. Wakagi, T. Koseki, S. Fushinobu
Crystal Structure Of A Feruloyl Esterase Belonging To The Tannase Family: A Disulfide Bond Near A Catalytic Triad
Proteins 2014
PubMed: search  |  Reference-DOI: 10.1002/PROT.24649
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE FERULOYL ESTERASE B-1
    Chains: A, B
    EC Number: 3.1.1.73
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: KM71H
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: AO090001000066, AOFAEB, FAEB-1
    Organism Common: YELLOW KOJI MOLD
    Organism Scientific: ASPERGILLUS ORYZAE
    Organism Taxid: 510516
    Strain: RIB 40
    Synonym: FERULIC ACID ESTERASE B-1, FAEB-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:272 , ASP A:275 , ALA A:277 , ASP A:279 , ILE A:281 , HOH A:705BINDING SITE FOR RESIDUE CA A 606
02AC2SOFTWAREASP B:272 , ASP B:275 , ALA B:277 , ASP B:279 , ILE B:281 , HOH B:710BINDING SITE FOR RESIDUE CA B 604
03AC3SOFTWAREASN A:49 , HOH A:766 , HOH A:900 , HOH A:1006 , HOH A:1102 , HOH A:1120 , LYS B:408 , GLY B:494 , PRO B:528 , GLY B:529 , HOH B:828 , HOH B:1005BINDING SITE FOR MONO-SACCHARIDE NAG A 601 BOUND TO ASN A 49
04AC4SOFTWAREHIS A:56 , ASN A:95 , GLN A:103 , PHE A:105 , ASN A:149 , GLY A:151 , HIS A:152 , HOH A:963BINDING SITE FOR MONO-SACCHARIDE NAG A 602 BOUND TO ASN A 95
05AC5SOFTWAREASN A:231 , ASN A:234 , PHE A:331 , LEU A:332 , ALA A:382 , ASN A:385 , TRP A:395 , HOH A:1226 , HOH A:1255BINDING SITE FOR MONO-SACCHARIDE NAG A 603 BOUND TO ASN A 234
06AC6SOFTWARELEU A:296 , ASN A:298 , GLN A:301 , HOH A:968 , HOH A:1008 , HOH A:1040 , HOH A:1062 , HOH A:1139 , SER B:441BINDING SITE FOR MONO-SACCHARIDE NAG A 604 BOUND TO ASN A 298
07AC7SOFTWAREGLN A:162 , ASN A:367 , SER A:441 , ASP A:444 , ASP A:498 , LYS A:518 , HOH A:827 , HOH A:977 , HOH A:1014 , HOH A:1109BINDING SITE FOR MONO-SACCHARIDE NAG A 605 BOUND TO ASN A 367
08AC8SOFTWAREHIS B:56 , ASN B:95 , GLN B:103 , PHE B:105 , ASN B:149 , GLY B:151 , HIS B:152 , PHE B:153BINDING SITE FOR MONO-SACCHARIDE NAG B 601 BOUND TO ASN B 95
09AC9SOFTWAREASN B:231 , ASN B:234 , PHE B:331 , LEU B:332 , ASN B:385 , TRP B:395 , HOH B:756 , HOH B:1006 , HOH B:1182BINDING SITE FOR MONO-SACCHARIDE NAG B 602 BOUND TO ASN B 234
10BC1SOFTWAREGLN A:162 , SER A:441 , HOH A:977 , LEU B:296 , ASN B:298 , GLN B:301 , HOH B:740 , HOH B:967 , HOH B:978 , HOH B:993 , HOH B:1032BINDING SITE FOR MONO-SACCHARIDE NAG B 603 BOUND TO ASN B 298

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:41 -A:90
2A:76 -A:129
3A:202 -A:458
4A:271 -A:288
5A:297 -A:308
6A:517 -A:539
7B:41 -B:90
8B:202 -B:458
9B:271 -B:288
10B:297 -B:308
11B:517 -B:539

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:127 -Gly A:128
2Tyr A:519 -Pro A:520
3Gly A:527 -Pro A:528
4Gly B:127 -Gly B:128
5Tyr B:519 -Pro B:520
6Gly B:527 -Pro B:528

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WMT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WMT)

(-) Exons   (0, 0)

(no "Exon" information available for 3WMT)

(-) 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:503
 aligned with FAEB1_ASPOR | Q2UP89 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:505
                                    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     
          FAEB1_ASPOR    36 SFQAECESFKAKINVTNANVHSVTYVPAGVNISMADNPSICGGDEDPITSTFAFCRIALNVTTSSKSQIFMEAWLPSNYSGRFLSTGNGGLGGCVKYDDMAYAAGYGFATVGTNNGHFGNNGVSFYQNTEVVEDFAYRALHTGVVVGKELTKNFYPQGYNKSYYLGCSTGGRQGWKSVQTFPDDFDGVVAGAPAFNFINLTSWGARFLTLTGDSSAETFVTETQWTAVHNEIIRQCDSLDGAKDGIIEDPDLCQPIIEALLCNATQSSTSGTCLTGAQVKTVNGVFSATYGLNGSFLYPRMQPGSELAAYSSYYSGTPFAYAEDWYRYVVFNNTNWDVATWTVQDAAIANAQDPYQISTWNGDLSPFQKKGGKVLHYHGMEDAIISSESSKVYYKHVADTMNLSPSELDSFYRFFPISGMAHCANADGPSAIGQGTGTFAGNNPQDNVLLAMVQWVEEGVAPDFVRGAKLNGSTVEYRRKHCKYPKRNRYVGPGSYTDENAWECV 540
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....eeeeeeeee...........hhhhh..--.......eeeeeeeeeee..eeeeeeeeee......eee..........hhhhhhhhhh...eeeee........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhhh.....hhhhh...hhhhhhhhhhhh..ee.hhh.eee......hhhhhhhhh.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhh.hhhhhh..eeeeee.................hhhhh...hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeee....eeee.......hhh.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wmt A  36 SFQAECESFKAKINVTNANVHSVTYVPAGVNISMADNPSICGGD--PITSTFAFCRIALNVTTSSKSQIFMEAWLPSNYSGRFLSTGNGGLGGCVKYDDMAYAAGYGFATVGTNNGHFGNNGVSFYQNTEVVEDFAYRALHTGVVVGKELTKNFYPQGYNKSYYLGCSTGGRQGWKSVQTFPDDFDGVVAGAPAFNFINLTSWGARFLTLTGDSSAETFVTETQWTAVHNEIIRQCDSLDGAKDGIIEDPDLCQPIIEALLCNATQSSTSGTCLTGAQVKTVNGVFSATYGLNGSFLYPRMQPGSELAAYSSYYSGTPFAYAEDWYRYVVFNNTNWDVATWTVQDAAIANAQDPYQISTWNGDLSPFQKKGGKVLHYHGMEDAIISSESSKVYYKHVADTMNLSPSELDSFYRFFPISGMAHCANADGPSAIGQGTGTFAGNNPQDNVLLAMVQWVEEGVAPDFVRGAKLNGSTVEYRRKHCKYPKRNRYVGPGSYTDENAWECV 540
                                    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     
                                                                      79 82                                                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:498
 aligned with FAEB1_ASPOR | Q2UP89 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:505
                                    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     
          FAEB1_ASPOR    36 SFQAECESFKAKINVTNANVHSVTYVPAGVNISMADNPSICGGDEDPITSTFAFCRIALNVTTSSKSQIFMEAWLPSNYSGRFLSTGNGGLGGCVKYDDMAYAAGYGFATVGTNNGHFGNNGVSFYQNTEVVEDFAYRALHTGVVVGKELTKNFYPQGYNKSYYLGCSTGGRQGWKSVQTFPDDFDGVVAGAPAFNFINLTSWGARFLTLTGDSSAETFVTETQWTAVHNEIIRQCDSLDGAKDGIIEDPDLCQPIIEALLCNATQSSTSGTCLTGAQVKTVNGVFSATYGLNGSFLYPRMQPGSELAAYSSYYSGTPFAYAEDWYRYVVFNNTNWDVATWTVQDAAIANAQDPYQISTWNGDLSPFQKKGGKVLHYHGMEDAIISSESSKVYYKHVADTMNLSPSELDSFYRFFPISGMAHCANADGPSAIGQGTGTFAGNNPQDNVLLAMVQWVEEGVAPDFVRGAKLNGSTVEYRRKHCKYPKRNRYVGPGSYTDENAWECV 540
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....eeeeeeeee.............-------.......eeeeeeeeeee..eeeeeeeeee......eee..........hhhhhhhhhh...eeeee........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhhh.....hhhhh...hhhhhhhhhhhh..ee.hhh.eee......hhhhhhhhh.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhh.hhhhhh..eeeeee.................hhhhh...hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeee.....eee.......hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wmt B  36 SFQAECESFKAKINVTNANVHSVTYVPAGVNISMADNPS-------PITSTFAFCRIALNVTTSSKSQIFMEAWLPSNYSGRFLSTGNGGLGGCVKYDDMAYAAGYGFATVGTNNGHFGNNGVSFYQNTEVVEDFAYRALHTGVVVGKELTKNFYPQGYNKSYYLGCSTGGRQGWKSVQTFPDDFDGVVAGAPAFNFINLTSWGARFLTLTGDSSAETFVTETQWTAVHNEIIRQCDSLDGAKDGIIEDPDLCQPIIEALLCNATQSSTSGTCLTGAQVKTVNGVFSATYGLNGSFLYPRMQPGSELAAYSSYYSGTPFAYAEDWYRYVVFNNTNWDVATWTVQDAAIANAQDPYQISTWNGDLSPFQKKGGKVLHYHGMEDAIISSESSKVYYKHVADTMNLSPSELDSFYRFFPISGMAHCANADGPSAIGQGTGTFAGNNPQDNVLLAMVQWVEEGVAPDFVRGAKLNGSTVEYRRKHCKYPKRNRYVGPGSYTDENAWECV 540
                                    45        55        65        |-      | 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     
                                                                 74      82
   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  (0, 0)

(no "SCOP Domain" information available for 3WMT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WMT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WMT)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FAEB1_ASPOR | Q2UP89)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0030600    feruloyl esterase activity    Catalysis of the reaction: feruloyl-polysaccharide + H2O = ferulate + polysaccharide.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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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