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(-) Description

Title :  STRUCTURE OF THE E242A MUTANT OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM GRAMINEARUM IN COMPLEX 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) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydrolase, Glycosyl 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, B, C
    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
    Mutation: YES
    Organism Scientific: GIBBERELLA ZEAE
    Organism Taxid: 5518
    Synonym: ALPHA-L-ARABINOFURANOSIDASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1AHR3Ligand/IonALPHA-L-ARABINOFURANOSE
2CA3Ligand/IonCALCIUM ION
3EDG3Ligand/Ion1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AHR1Ligand/IonALPHA-L-ARABINOFURANOSE
2CA-1Ligand/IonCALCIUM ION
3EDG1Ligand/Ion1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AHR1Ligand/IonALPHA-L-ARABINOFURANOSE
2CA-1Ligand/IonCALCIUM ION
3EDG1Ligand/Ion1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1AHR1Ligand/IonALPHA-L-ARABINOFURANOSE
2CA-1Ligand/IonCALCIUM ION
3EDG1Ligand/Ion1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:161 , TRP A:169 , GLU A:170 , GLN A:195 , ARG A:223 , GLY A:225 , MET A:226 , TYR A:337 , AHR A:501 , HOH A:2373BINDING SITE FOR RESIDUE EDG A 500
2AC2SOFTWAREGLU A:60 , GLN A:101 , PRO A:161 , TRP A:169 , EDG A:500 , HOH A:2085 , HOH A:2140 , HOH A:2142 , HOH A:2400 , HOH A:2401BINDING SITE FOR RESIDUE AHR A 501
3AC3SOFTWAREASP A:32 , PRO A:33 , HOH A:2024 , HOH A:2025 , HOH A:2029 , ASN B:248BINDING SITE FOR RESIDUE CA A 502
4AC4SOFTWARETRP B:169 , GLU B:170 , SER B:185 , GLN B:187 , GLN B:195 , ARG B:223 , GLY B:225 , MET B:226 , TYR B:337 , AHR B:501 , HOH B:2257BINDING SITE FOR RESIDUE EDG B 500
5AC5SOFTWAREGLU B:60 , GLN B:101 , PRO B:161 , EDG B:500 , HOH B:2046 , HOH B:2088 , HOH B:2091 , HOH B:2274 , HOH B:2275BINDING SITE FOR RESIDUE AHR B 501
6AC6SOFTWAREASP B:32 , PRO B:33 , HOH B:2006 , ASN C:248 , HOH C:2208BINDING SITE FOR RESIDUE CA B 502
7AC7SOFTWAREPRO C:161 , TRP C:169 , GLU C:170 , SER C:185 , GLN C:195 , ARG C:223 , GLY C:225 , MET C:226 , TYR C:337 , AHR C:501 , HOH C:2268BINDING SITE FOR RESIDUE EDG C 500
8AC8SOFTWAREGLU C:60 , GLN C:101 , PRO C:161 , TRP C:169 , EDG C:500 , HOH C:2061 , HOH C:2102 , HOH C:2105 , HOH C:2287 , HOH C:2288BINDING SITE FOR RESIDUE AHR C 501
9AC9SOFTWAREASN A:248 , HOH A:2287 , HOH A:2289 , HOH A:2290 , ASP C:32 , PRO C:33 , HOH C:2009BINDING SITE FOR RESIDUE CA C 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric 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
5Asp B:39 -Pro B:40
6Glu B:65 -Pro B:66
7Pro B:66 -Pro B:67
8Pro B:360 -Pro B:361
9Asp C:39 -Pro C:40
10Glu C:65 -Pro C:66
11Pro C:66 -Pro C:67
12Pro C:360 -Pro C:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YDP)

(-) Sequences/Alignments

Asymmetric 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:361
 aligned with B8ZY56_GIBZA | B8ZY56 from UniProtKB/TrEMBL  Length:365

    Alignment length:361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
         B8ZY56_GIBZA     4 QKGKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWFPIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLCSGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEPFLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYYARPGMPTVAKLPNNEYIYVYEYGGGPNPPAGSDYWFPVYYRLSKDPQKFLNKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALGDASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSASVVRLSEVMK 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
                 2ydp A  20 QKGKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWFPIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLCSGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEPFLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYYARPGMPTVAKLPNNEYIYVYAYGGGPNPPAGSDYWFPVYYRLSKDPQKFLNKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALGDASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSASVVRLSEVMK 380
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379 


Chain B 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..........eeee......eeeeee............eeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ydp B  22 GKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWFPIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLCSGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEPFLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYYARPGMPTVAKLPNNEYIYVYAYGGGPNPPAGSDYWFPVYYRLSKDPQKFLNKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALGDASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSASVVRLSEVMK 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         


Chain C 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..........eeee......eeeeee............eeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ydp C  22 GKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWFPIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLCSGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEPFLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYYARPGMPTVAKLPNNEYIYVYAYGGGPNPPAGSDYWFPVYYRLSKDPQKFLNKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALGDASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSASVVRLSEVMK 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 2YDP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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

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

UniProtKB/TrEMBL
        B8ZY56_GIBZA | B8ZY56: 2ydt 5m1z

(-) Related Entries Specified in the PDB File

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