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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABINOFURANOSIDASE COMPLEXED WITH ARABINOFURANOSYL-ALPHA-1,2-XYLOBIOSE
 
Authors :  A. Miyanaga, T. Koseki, Y. Miwa, H. Matsuzawa, T. Wakagi, H. Shoun, S. Fu
Date :  07 Oct 05  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Arabinofuranosyl-Alpha-1, 2-Xylobiose Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Miyanaga, T. Koseki, Y. Miwa, Y. Mese, S. Nakamura, A. Kuno, J. Hirabayashi, H. Matsuzawa, T. Wakagi, H. Shoun, S. Fushinobu
The Family 42 Carbohydrate-Binding Module Of Family 54 Alpha-L-Arabinofuranosidase Specifically Binds The Arabinofuranose Side Chain Of Hemicellulose
Biochem. J. V. 399 503 2006
PubMed-ID: 16846393  |  Reference-DOI: 10.1042/BJ20060567

(-) Compounds

Molecule 1 - ALPHA-L-ARABINOFURANOSIDASE B
    Chains: A
    EC Number: 3.2.1.55
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZAC
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 19-499
    Mutation: YES
    Organism Scientific: ASPERGILLUS KAWACHII
    Organism Taxid: 40384

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1AHR2Ligand/IonALPHA-L-ARABINOFURANOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3XYS4Ligand/IonXYLOPYRANOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:174 , ASN A:202 , THR A:204 , NAG A:502BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWARETHR A:429 , LYS A:430 , NAG A:501BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREHIS A:416 , TYR A:417 , ASN A:418 , PHE A:419 , GLN A:431 , ASP A:435 , XYS A:701 , XYS A:702 , HOH A:746BINDING SITE FOR RESIDUE AHR A 700
4AC4SOFTWARETYR A:417 , AHR A:700 , XYS A:702BINDING SITE FOR RESIDUE XYS A 701
5AC5SOFTWAREPRO A:142 , PHE A:419 , TYR A:456 , AHR A:700 , XYS A:701 , HOH A:749BINDING SITE FOR RESIDUE XYS A 702
6AC6SOFTWARETHR A:356 , TYR A:359 , HIS A:463 , TYR A:464 , GLU A:465 , ASN A:466 , ASP A:488 , XYS A:711 , XYS A:712 , HOH A:786BINDING SITE FOR RESIDUE AHR A 710
7AC7SOFTWAREGLU A:465 , AHR A:710 , XYS A:712BINDING SITE FOR RESIDUE XYS A 711
8AC8SOFTWARETYR A:359 , GLU A:465 , ASN A:466 , AHR A:710 , XYS A:711BINDING SITE FOR RESIDUE XYS A 712

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:31
2A:81 -A:86
3A:176 -A:177
4A:401 -A:439

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Cys A:176 -Cys A:177
2Gly A:213 -Pro A:214
3Asn A:282 -Pro A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D44)

(-) Exons   (0, 0)

(no "Exon" information available for 2D44)

(-) 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:482
 aligned with ABFB_ASPKW | Q8NK89 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:482
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497  
           ABFB_ASPKW    18 AGPCDIYEAGDTPCVAAHSTTRALYSSFSGALYQLQRGSDDTTTTISPLTAGGIADASAQDTFCANTTCLITIIYDQSGNGNHLTQAPPGGFDGPDTDGYDNLASAIGAPVTLNGQKAYGVFMSPGTGYRNNEATGTATGDEAEGMYAVLDGTHYNDACCFDYGNAETSSTDTGAGHMEAIYLGNSTTWGYGAGDGPWIMVDMENNLFSGADEGYNSGDPSISYRFVTAAVKGGADKWAIRGANAASGSLSTYYSGARPDYSGYNPMSKEGAIILGIGGDNSNGAQGTFYEGVMTSGYPSDDTENSVQENIVAAKYVVGSLVSGPSFTSGEVVSLRVTTPGYTTRYIAHTDTTVNTQVVDDDSSTTLKEEASWTVVTGLANSQCFSFESVDTPGSYIRHYNFELLLNANDGTKQFHEDATFCPQAALNGEGTSLRSWSYPTRYFRHYENVLYAASNGGVQTFDSKTSFNNDVSFEIETAFAS 499
               SCOP domains d2d44a1 A:18-337 automated matches                                                                                                                                                                                                                                                                                              d2d44a2 A:338-499 automated matches                                                                                                                                SCOP domains
               CATH domains 2d44A01 A:18-337  [code=2.60.120.200, no name defined]                                                                                                                                                                                                                                                                          2d44A02 A:338-499  [code=2.80.10.50, no name defined]                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee.............eeeee.....eeee.........hhhhhhhhh....eeeeee.........eee.........hhhhh...ee...eeeee..eeeeeeee.....eee............eeeeeee...........eeeee............eeeeee.............eeeee....ee..................eeeeeeee..eeeeeeee..eeeeeeeeee...............eeee...........eeeeeeeeee...hhhhhhhhhhhhhhhheee.............eeeeee.......eeeeee..eeeeee.....hhhhhhhh.eeeee.......eeeee.....eeeeee..eeeeee...hhhhhhhh.eeeee......eeeee.....eeeeee..eeeeee....hhhhh..hhhhhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d44 A  18 MGPCDIYEAGDTPCVAAHSTTRALYSSFSGALYQLQRGSDDTTTTISPLTAGGIADASAQDTFCANTTCLITIIYDQSGNGNHLTQAPPGGFDGPDTDGYDNLASAIGAPVTLNGQKAYGVFMSPGTGYRNNEATGTATGDEAEGMYAVLDGTHYNDACCFDYGNAETSSTDTGAGHMEAIYLGNSTTWGYGAGDGPWIMVDMANNLFSGADEGYNSGDPSISYRFVTAAVKGGADKWAIRGANAASGSLSTYYSGARPDYSGYNPMSKEGAIILGIGGDNSNGAQGTFYEGVMTSGYPSDDTENSVQENIVAAKYVVGSLVSGPSFTSGEVVSLRVTTPGYTTRYIAHTDTTVNTQVVDDDSSTTLKEEASWTVVTGLANSQCFSFESVDTPGSYIRHYNFELLLNANDGTKQFHEDATFCPQAALNGEGTSLRSWSYPTRYFRHYENVLYAASNGGVQTFDSKTSFNNDVSFEIETAFAS 499
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D44)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ABFB_ASPKW | Q8NK89)
molecular function
    GO:0046556    alpha-L-arabinofuranosidase activity    Catalysis of the hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.
    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.
biological process
    GO:0046373    L-arabinose metabolic process    The chemical reactions and pathways involving L-arabinose, the D-enantiomer of arabino-pentose. L-arabinose occurs free, e.g. in the heartwood of many conifers, and in the combined state, in both furanose and pyranose forms, as a constituent of various plant hemicelluloses, bacterial polysaccharides etc.
    GO:0031222    arabinan catabolic process    The chemical reactions and pathways resulting in the breakdown of arabinan, a polysaccharide composed of arabinose residues.
    GO:0031221    arabinan metabolic process    The chemical reactions and pathways involving arabinan, a polysaccharide composed of arabinose residues.
    GO:0019566    arabinose metabolic process    The chemical reactions and pathways involving arabinose, arabino-pentose. L-Arabinose occurs both free, for example in the heartwood of many conifers, and in the combined state, as a constituent of plant hemicelluloses, bacterial polysaccharides etc. D-arabinose is a constituent of arabinonucleosides.
    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.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        ABFB_ASPKW | Q8NK89: 1wd3 1wd4 2d43

(-) Related Entries Specified in the PDB File

1wd3
1wd4
2d43 THE SAME PROTEIN COMPLEXED WITH ARABINOTRIOSE