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(-) Description

Title :  STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM GRAMINEARUM IN COMPLEXE WITH AN IMINOSUGAR INHIBITOR
 
Authors :  E. D. Goddard-Borger, R. Carapito, J. M. Jeltsch, V. Phalip, R. V. Stick
Date :  24 Mar 11  (Deposition) - 13 Jul 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. D. Goddard-Borger, R. Carapito, J. Jeltsch, V. Phalip, R. V. Stick, A. Varrot
Alpha-L-Arabinofuranosylated Pyrrolidines As Arabinanase Inhibitors.
Chem. Commun. (Camb. ) V. 47 9684 2011
PubMed-ID: 21773614  |  Reference-DOI: 10.1039/C1CC13675E

(-) Compounds

Molecule 1 - EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
    Chains: A
    EC Number: 3.2.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET30A
    Expression System Vector Type: PLASMID
    Organism Scientific: GIBBERELLA ZEAE
    Organism Taxid: 5518
    Synonym: ALPHA-L-ARABINOFURANOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2AHR1Ligand/IonALPHA-L-ARABINOFURANOSE
3EDG1Ligand/Ion1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
4MN5Ligand/IonMANGANESE (II) ION
5SO45Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:161 , TRP A:169 , GLU A:170 , SER A:185 , GLN A:187 , GLN A:195 , ARG A:223 , GLY A:225 , MET A:226 , GLU A:242 , TYR A:337 , AHR A:501 , ACT A:1512 , HOH A:2481BINDING SITE FOR RESIDUE EDG A 500
02AC2SOFTWAREGLU A:60 , GLN A:101 , PRO A:161 , TRP A:169 , EDG A:500 , HOH A:2121 , HOH A:2197 , HOH A:2200 , HOH A:2513 , HOH A:2514BINDING SITE FOR RESIDUE AHR A 501
03AC3SOFTWAREGLY A:22 , LYS A:23 , THR A:24 , ARG A:374 , HOH A:2005 , HOH A:2512BINDING SITE FOR RESIDUE SO4 A1502
04AC4SOFTWAREGLY A:157 , GLU A:158 , LEU A:165 , THR A:166 , HOH A:2253 , HOH A:2296 , HOH A:2305BINDING SITE FOR RESIDUE SO4 A1503
05AC5SOFTWARETHR A:35 , ASN A:219 , GLY A:364 , LYS A:365 , HOH A:2070 , HOH A:2361 , HOH A:2378 , HOH A:2380 , HOH A:2499 , HOH A:2515BINDING SITE FOR RESIDUE SO4 A1504
06AC6SOFTWARETHR A:175 , LYS A:177 , LYS A:231 , TYR A:237 , HOH A:2213 , HOH A:2309 , HOH A:2312 , HOH A:2516BINDING SITE FOR RESIDUE SO4 A1505
07AC7SOFTWARETYR A:105 , PRO A:108 , MET A:174 , THR A:175 , HOH A:2207 , HOH A:2307 , HOH A:2517 , HOH A:2518 , HOH A:2519BINDING SITE FOR RESIDUE SO4 A1506
08AC8SOFTWAREASP A:32 , HOH A:2024 , HOH A:2025 , HOH A:2026 , HOH A:2027 , HOH A:2499BINDING SITE FOR RESIDUE MN A1507
09AC9SOFTWAREGLN A:345 , HOH A:2088 , HOH A:2089 , HOH A:2521BINDING SITE FOR RESIDUE MN A1508
10BC1SOFTWAREGLU A:377 , HOH A:2005 , HOH A:2511 , HOH A:2512BINDING SITE FOR RESIDUE MN A1509
11BC2SOFTWAREASP A:32 , HOH A:2018 , HOH A:2028 , HOH A:2522BINDING SITE FOR RESIDUE MN A1510
12BC3SOFTWAREGLU A:313 , ASP A:330 , HOH A:2460BINDING SITE FOR RESIDUE MN A1511
13BC4SOFTWAREGLU A:242 , GLY A:288 , EDG A:500 , HOH A:2432 , HOH A:2481 , HOH A:2524BINDING SITE FOR RESIDUE ACT A1512

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:39 -Pro A:40
2Glu A:65 -Pro A:66
3Pro A:66 -Pro A:67
4Pro A:360 -Pro A:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YDT)

(-) 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:359
 aligned with B8ZY56_GIBZA | B8ZY56 from UniProtKB/TrEMBL  Length:365

    Alignment length:359
                                    15        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         
         B8ZY56_GIBZA     6 GKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWFPIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLCSGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEPFLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYYARPGMPTVAKLPNNEYIYVYEYGGGPNPPAGSDYWFPVYYRLSKDPQKFLNKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALGDASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSASVVRLSEVMK 364
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..........eeeeeeee.....eeeeeee.........eeeeee.......eeeeee........eeeeeeeee............eeeeeee.......eeeeeeee.......eeeeeeeee...........eeeeeeeee..eeeeeeee.........eeeeeee.........eeee.......eeeeeeeee.....eeeeeeee..............eeeeee...........eee............eeeee.......eeeee......eeee........eeee..........eeeee.....eeeeee............eeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ydt A  22 GKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWFPIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLCSGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEPFLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYYARPGMPTVAKLPNNEYIYVYEYGGGPNPPAGSDYWFPVYYRLSKDPQKFLNKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALGDASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSASVVRLSEVMK 380
                                    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       321       331       341       351       361       371
   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 2YDT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YDT)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B8ZY56_GIBZA | B8ZY56)
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: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.

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 Related Entries

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        B8ZY56_GIBZA | B8ZY56: 2ydp 5m1z

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2ydp STRUCTURE OF THE E242A MUTANT OF THE ALPHA-L- ARABINOFURANOSIDASE ARB93A FROM FUSARIUM GRAMINEARUM IN COMPLEXE WITH AN IMINOSUGAR INHIBITOR