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(-) Description

Title :  STRUCTURE OF THE THERMOSTABLE ARABINANASE
 
Authors :  A. Yamaguchi, T. Tada, T. Nakaniwa, T. Kitatani
Date :  21 Jun 04  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Arabinanase, Abn-Ts, Thermostable Enzyme, Glycoside Hydrolase, Bacillus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yamaguchi, T. Tada, K. Wada, T. Nakaniwa, T. Kitatani, Y. Sogabe, M. Takao, T. Sakai, K. Nishimura
Structural Basis For Thermostability Of Endo-1, 5-Alpha-L-Arabinanase From Bacillus Thermodenitrificans Ts-3.
J. Biochem. (Tokyo) V. 137 587 2005
PubMed-ID: 15944411  |  Reference-DOI: 10.1093/JB/MVI078
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARABINANASE-TS
    Chains: A
    EC Number: 3.2.1.99
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PUB110
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS
    Organism Taxid: 33940
    Strain: TS-3
    Synonym: ENDO-1,5-ALPHA-L-ARABINANASE, ARABINASE-TS, RABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:271 , HOH A:317 , HOH A:321 , HOH A:338 , HOH A:343 , HOH A:374 , HOH A:412BINDING SITE FOR RESIDUE CA A 314

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:221 -A:222

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:196 -Pro A:197
2Gly A:241 -Pro A:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WL7)

(-) Exons   (0, 0)

(no "Exon" information available for 1WL7)

(-) 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:312
 aligned with IABN_GEOTD | Q93HT9 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:312
                                    11        21        31        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  
           IABN_GEOTD     2 VHFHPFGNVNFYEMDWSLKGDLWAHDPVIAKEGSRWYVFHTGSGIQIKTSEDGVHWENMGRVFPSLPDWCKQYVPEKDEDHLWAPDICFYNGIYYLYYSVSTFGKNTSVIGLATNRTLDPRDPDYEWKDMGPVIHSTASDNYNAIDPNVVFDQEGQPWLSFGSFWSGIQLIQLDTETMKPAAQAELLTIASRGEEPNAIEAPFIVCRNGYYYLFVSFDFCCRGIESTYKIAVGRSKDITGPYVDKNGVSMMQGGGTILDAGNDRWIGPGHCAVYFSGVSAILVNHAYDALKNGEPTLQIRPLYWDDEGWPYL 313
               SCOP domains d1wl7a1 A:2-313 Arabinanase-TS                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1wl7A00 A:2-313 Glycosyl hydrolase domain; family 43                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee.......eeeee..eeeeee.ee..eeeee....eeeeeee.......hhhhhh......eeeeeeeeee..eeeeeeee.......eeeeeeee............eeeeeeeee...........eeee.....eeeee......eeeee..............eeee........eeeeeeeee..eeeeeeee....hhhhh..eeeeeee.............hhhhh..eeee.....eeeeeeeeeeee..eeeeeeeeee......eeeeeee.ee.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wl7 A   2 VHFHPFGNVNFYEMDWSLKGDLWAHDPVIAKEGSRWYVFHTGSGIQIKTSEDGVHWENMGRVFPSLPDWCKQYVPEKDEDHLWAPDICFYNGIYYLYYSVSTFGKNTSVIGLATNRTLDPRDPDYEWKDMGPVIHSTASDNYNAIDPNVVFDQEGQPWLSFGSFWSGIQLIQLDTETMKPAAQAELLTIASRGEEPNAIEAPFIVCRNGYYYLFVSFDFCCRGIESTYKIAVGRSKDITGPYVDKNGVSMMQGGGTILDAGNDRWIGPGHCAVYFSGVSAILVNHAYDALKNGEPTLQIRPLYWDDEGWPYL 313
                                    11        21        31        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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WL7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IABN_GEOTD | Q93HT9)
molecular function
    GO:0046558    arabinan endo-1,5-alpha-L-arabinosidase activity    Catalysis of the endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5) arabinans.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0031222    arabinan catabolic process    The chemical reactions and pathways resulting in the breakdown of arabinan, a polysaccharide composed of arabinose residues.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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