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(-) Description

Title :  THE STRUCTURE AND FUNCTION OF AN ARABINAN-SPECIFIC ALPHA-1,2-ARABINOFURANOSIDASE IDENTIFIED FROM SCREENING THE ACTIVITIES OF BACTERIAL GH43 GLYCOSIDE HYDROLASES
 
Authors :  A. Cartmell, L. S. Mckee, M. Pena, J. Larsbrink, H. Brumer, R. J. Lewis, A Nielsen, H. J. Gilbert, J. Marles-Wright
Date :  20 Jan 11  (Deposition) - 16 Feb 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  5-Bladed Beta Propeller, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Cartmell, L. S. Mckee, M. J. Pena, J. Larsbrink, H. Brumer, S. Kaneko H. Ichinose, R. J. Lewis, A. Vikso-Nielsen, H. J. Gilbert, J. Marles-Wright
The Structure And Function Of An Arabinan-Specific {Alpha}-1, 2-Arabinofuranosidase Identified From Screening The Activities Of Bacterial Gh43 Glycoside Hydrolases.
J. Biol. Chem. V. 286 15483 2011
PubMed-ID: 21339299  |  Reference-DOI: 10.1074/JBC.M110.215962

(-) Compounds

Molecule 1 - BETA-XYLOSIDASE/ALPHA-L-ARABINFURANOSIDASE, GLY43N
    Chains: A, B
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 28-334
    Gene: GLY43N, CJA_3018
    Mutation: YES
    Organism Common: PSEUDOMONAS FLUORESCENS SUBSP. CELLULOSA
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 498211
    Strain: UEDA107

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1AHR7Ligand/IonALPHA-L-ARABINOFURANOSE
2CA2Ligand/IonCALCIUM ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AHR3Ligand/IonALPHA-L-ARABINOFURANOSE
2CA-1Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1AHR4Ligand/IonALPHA-L-ARABINOFURANOSE
2CA-1Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:154 , THR A:157 , ASP A:165 , ASP A:166 , HOH A:363BINDING SITE FOR RESIDUE CA A 335
02AC2SOFTWAREPHE A:67 , MET A:69 , TRP A:103 , ARG A:295 , AHR A:338 , HOH A:459 , HOH A:512 , HOH A:620BINDING SITE FOR RESIDUE EDO A 336
03AC3SOFTWARETRP A:164 , ASN A:185 , PHE A:234 , AHR A:338 , HOH A:398BINDING SITE FOR RESIDUE AHR A 337
04AC4SOFTWAREASN A:185 , THR A:214 , GLU A:215 , EDO A:336 , AHR A:337 , AHR A:339BINDING SITE FOR RESIDUE AHR A 338
05AC5SOFTWARETRP A:164 , AHR A:338 , HOH A:559BINDING SITE FOR RESIDUE AHR A 339
06AC6SOFTWAREASN B:154 , THR B:157 , ASP B:165 , ASP B:166 , HOH B:457BINDING SITE FOR RESIDUE CA B 335
07AC7SOFTWAREPHE B:67 , MET B:69 , TRP B:103 , ARG B:295 , AHR B:338 , HOH B:546 , HOH B:547 , HOH B:548BINDING SITE FOR RESIDUE EDO B 336
08AC8SOFTWARELYS A:195 , TRP B:164 , ASN B:185 , PHE B:234 , AHR B:338 , AHR B:339 , AHR B:340BINDING SITE FOR RESIDUE AHR B 337
09AC9SOFTWAREPHE B:67 , ASN B:185 , THR B:214 , GLU B:215 , EDO B:336 , AHR B:337 , AHR B:339 , AHR B:340BINDING SITE FOR RESIDUE AHR B 338
10BC1SOFTWAREASN A:111 , PHE B:66 , TRP B:164 , AHR B:337 , AHR B:338 , AHR B:340BINDING SITE FOR RESIDUE AHR B 339
11BC2SOFTWAREASN A:111 , PHE B:67 , PHE B:234 , PRO B:264 , THR B:265 , GLN B:292 , TYR B:293 , AHR B:337 , AHR B:338 , AHR B:339BINDING SITE FOR RESIDUE AHR B 340

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QEF)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Asn A:31 -Pro A:32
2Gly A:141 -Pro A:142
3Phe A:234 -Pro A:235
4Gly A:248 -Pro A:249
5Arg A:287 -Pro A:288
6Asn B:31 -Pro B:32
7Gly B:141 -Pro B:142
8Phe B:234 -Pro B:235
9Gly B:248 -Pro B:249
10Arg B:287 -Pro B:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QEF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QEF)

(-) 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:296
 aligned with B3PD60_CELJU | B3PD60 from UniProtKB/TrEMBL  Length:334

    Alignment length:296
                                    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      
         B3PD60_CELJU    30 ENPIFTDVFTADPAALVHKGRVYLYAGRDEAPDNTTFFVMNEWLVYSSDDMANWEAHGPGLRAKDFTWAKGDAWASQVIERNGKFYWYVTVRHDDTKPGFAIGVAVGDSPIGPFKDALGKALITNDMTTDTPIDWDDIDPSVFIDDDGQAYLFWGNTRPRYAKLKKNMVELDGPIRAIEGLPEFTEAIWVHKYQDNYYLSYAMGFPEKIGYAMGKSIKGPWVYKGILNEVAGNTPTNHQAIIEFNNKHYFIYHTGAGRPDGGQYRRSVSIDELFYNPDGTIKRIVMTTEGVAPNKS 325
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeeee..........eeeeeeeee......eeeeeeee.hhh..eeeeeeeeeeeee..eeeeeeeeee......eeeeeeee......eee.......hhhhh............eeee.....eeeee.....eeeee...........ee......eeeeeeeeee..eeeeeeee....eeeeeee.......eeeeeee...........eeeee..eeeeeeee............eeeeeee....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qef A  30 ENPIFTDVFTAAPAALVHKGRVYLYAGRDEAPDNTTFFVMNEWLVYSSDDMANWEAHGPGLRAKDFTWAKGDAWASQVIERNGKFYWYVTVRHDDTKPGFAIGVAVGDSPIGPFKDALGKALITNDMTTDTPIDWDDIDPSVFIDDDGQAYLFWGNTRPRYAKLKKNMVELDGPIRAIEGLPEFTEAIWVHKYQDNYYLSYAMGFPEKIGYAMGKSIKGPWVYKGILNEVAGNTPTNHQAIIEFNNKHYFIYHTGAGRPDGGQYRRSVSIDELFYNPDGTIKRIVMTTEGVAPNKS 325
                                    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      


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with B3PD60_CELJU | B3PD60 from UniProtKB/TrEMBL  Length:334

    Alignment length:297
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
         B3PD60_CELJU    29 AENPIFTDVFTADPAALVHKGRVYLYAGRDEAPDNTTFFVMNEWLVYSSDDMANWEAHGPGLRAKDFTWAKGDAWASQVIERNGKFYWYVTVRHDDTKPGFAIGVAVGDSPIGPFKDALGKALITNDMTTDTPIDWDDIDPSVFIDDDGQAYLFWGNTRPRYAKLKKNMVELDGPIRAIEGLPEFTEAIWVHKYQDNYYLSYAMGFPEKIGYAMGKSIKGPWVYKGILNEVAGNTPTNHQAIIEFNNKHYFIYHTGAGRPDGGQYRRSVSIDELFYNPDGTIKRIVMTTEGVAPNKS 325
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Glyco_hydro_43-3qefB01 B:29-310                                                                                                                                                                                                                                                           --------------- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_43-3qefB02 B:29-310                                                                                                                                                                                                                                                           --------------- Pfam domains (2)
         Sec.struct. author .........eeeeeeeeee..eeeeeeeee..........eeeeeeeee......eeeeeeee.hhh..eeeeeeeeeeeee..eeeeeeeeee......eeeeeeee......eee.......hhhhh............eeee.....eeeee.....eeeee...........ee......eeeeeeeeee..eeeeeeee....eeeeeee.......eeeeeee...........eeeee..eeeeeeee............eeeeeee....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qef B  29 AENPIFTDVFTAAPAALVHKGRVYLYAGRDEAPDNTTFFVMNEWLVYSSDDMANWEAHGPGLRAKDFTWAKGDAWASQVIERNGKFYWYVTVRHDDTKPGFAIGVAVGDSPIGPFKDALGKALITNDMTTDTPIDWDDIDPSVFIDDDGQAYLFWGNTRPRYAKLKKNMVELDGPIRAIEGLPEFTEAIWVHKYQDNYYLSYAMGFPEKIGYAMGKSIKGPWVYKGILNEVAGNTPTNHQAIIEFNNKHYFIYHTGAGRPDGGQYRRSVSIDELFYNPDGTIKRIVMTTEGVAPNKS 325
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318
   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  (0, 0)

(no "SCOP Domain" information available for 3QEF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QEF)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: B_Fructosidase (34)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (B3PD60_CELJU | B3PD60)
molecular function
    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: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.

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 Related Entries

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        B3PD60_CELJU | B3PD60: 3qed 3qee

(-) Related Entries Specified in the PDB File

3qed 3qee