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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF 1,5-ALPHA-ARABINANASE CATALYTIC MUTANT (ABNBE201A) COMPLEXED TO ARABINOTRIOSE
 
Authors :  A. Alhassid, A. Ben David, Y. Shoham, G. Shoham
Date :  18 May 08  (Deposition) - 21 Apr 09  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Arabinanase, Glycosyl Hydrolase, Beta-Propeller, Geobacillus Stearothermophilus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Alhassid, A. Ben-David, O. Tabachnikov, D. Libster, E. Naveh, G. Zolotnitsky, Y. Shoham, G. Shoham
Crystal Structure Of An Inverting Gh 43 1, 5-Alpha-L-Arabinanase From Geobacillus Stearothermophilus Complexed With Its Substrate
Biochem. J. V. 422 73 2009
PubMed-ID: 19505290  |  Reference-DOI: 10.1042/BJ20090180
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTRACELLULAR ARABINANASE
    Chains: A
    EC Number: 3.2.1.99
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ABN
    Mutation: YES
    Organism Common: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: T-6
    Synonym: 1,5-ALPHA-ARABINANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1AHR2Ligand/IonALPHA-L-ARABINOFURANOSE
2CA1Ligand/IonCALCIUM ION
3FUB1Ligand/IonBETA-L-ARABINOFURANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:105 , PHE A:165 , TRP A:166 , GLU A:196 , PRO A:197 , AHR A:403BINDING SITE FOR RESIDUE FUB A 402
2AC2SOFTWARETRP A:84 , PHE A:104 , GLY A:105 , ASN A:144 , SER A:164 , PHE A:165 , TRP A:166 , FUB A:402 , AHR A:404 , HOH A:658 , HOH A:659BINDING SITE FOR RESIDUE AHR A 403
3AC3SOFTWAREHIS A:26 , ASP A:27 , TRP A:84 , ASP A:147 , CYS A:221 , TYR A:229 , AHR A:403 , HOH A:643BINDING SITE FOR RESIDUE AHR A 404
4AC4SOFTWAREHIS A:271 , HOH A:502 , HOH A:504 , HOH A:532 , HOH A:569 , HOH A:610 , HOH A:637BINDING SITE FOR RESIDUE CA A 400

(-) 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 3D5Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D5Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3D5Z)

(-) 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:314
 aligned with IABN_GEOSE | B3EYM8 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:314
                                    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_GEOSE     2 VHFHPFGNVNFYEMDWSLKGDLWAHDPVIAKEGSRWYVFHTGSGIQIKTSEDGVHWENMGWVFPSLPDWYKQYVPEKDEDHLWAPDICFYNGIYYLYYSVSTFGKNTSVIGLATNQTLDPRDPDYEWKDMGPVIHSTASDNYNAIDPNVVFDQEGQPWLSFGSFWSGIQLIQLDTETMKPAAQAELLTIASRGEEPNAIEAPFIVCRNGYYYLFVSFDFCCRGIESTYKIAVGRSKDITGPYVDKNGVSMMQGGGTILDEGNDRWIGPGHCAVYFSGVSAILVNHAYDALKNGEPTLQIRPLYWDDEGWPYLSV 315
               SCOP domains d3d5za_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3d5zA00 A:2-315 Glycosyl hydrolase domain; family 43                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh....ee.......eeeee..eeeeee.ee..eeeee....eeeeeee.....hhhhhhh.......eeeeeeeeee..eeeeeeee.......eeeeeeee............eeeeeeeee...........eeee.....eeeee......eeeee..............eeee........eeeeeeeee..eeeeeeee....hhhhh..eeeeeee.............hhhhh..eeee.....eeeeeeeeeeee..eeeeeeeeee......eeeeeeeeee.....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d5z A   2 VHFHPFGGVNFYEMDWSLKGDLWAHDPVIAKEGSRWYVFHTGSGIQIKTSEDGVHWENMGWVFPSLPDWYKQYVPEKDEDHLWAPDICFYNGIYYLYYSVSTFGKNTSVIGLATNQTLDPRDPDYEWKDMGPVIHSTASDNYNAIDPNVVFDQEGQPWLSFGSFWSGIQLIQLDTETMKPAAQAELLTIASRGEEPNAIAAPFIVCRNGYYYLFVSFDFCCRGIESTYKIAVGRSKDITGPYVDKNGVSMMQGGGTILDEGNDRWIGPGHCAVYFSGVSAILVNHAYDALKNGEPTLQIRPLYWDDEGWPYLSV 315
                                    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)
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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 3D5Z)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IABN_GEOSE | B3EYM8)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        IABN_GEOSE | B3EYM8: 3cu9 3d5y 3d60 3d61

(-) Related Entries Specified in the PDB File

3cu9 1,5-ALPHA-ARABINANASE, NATIVE FORM
3d5y 1,5-ALPHA-ARABINANASE, CATALYTIC MUTANT E201A
3d60 1,5-ALPHA-ARABINANASE, CATALYTIC MUTANT D27A
3d61 1,5-ALPHA-ARABINANASE, CATALYTIC MUTANT D147A COMPLEXED TO ARABINOBIOSE