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(-) Description

Title :  UNDERSTANDING HOW DIVERSE MANNANASES RECOGNISE HETEROGENEOUS SUBSTRATES
 
Authors :  L. E. Tailford, V. M. A. Ducros, J. E. Flint, S. M. Roberts, C. Morland, D. L. Zechel, N. Smith, M. E. Bjornvad, T. V. Borchert, K. S. Wilson, G. J. Davies, H. J. Gilbert
Date :  05 May 09  (Deposition) - 26 May 09  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Mannanase, Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Tailford, V. M. A. Ducros, J. E. Flint, S. M. Roberts, C. Morland, D. L. Zechel, N. Smith, M. E. Bjornvad, T. V. Borchert, K. S. Wilson, G. J. Davies, H. J. Gilbert
Understanding How Diverse -Mannanases Recognise Heterogeneous Substrates.
Biochemistry V. 48 7009 2009
PubMed-ID: 19441796  |  Reference-DOI: 10.1021/BI900515D

(-) Compounds

Molecule 1 - BETA-MANNANASE
    Chains: A
    EC Number: 3.2.1.78
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Expression System Vector: PMOL944
    Fragment: RESIDUES 35-330
    Mutation: YES
    Organism Scientific: BACILLUS AGARADHAERENS
    Organism Taxid: 76935
    Strain: NCIMB 40482
    Synonym: BAMAN5

 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
1ACT1Ligand/IonACETATE ION
2BMA2Ligand/IonBETA-D-MANNOSE
3MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:80 , ARG A:93 , ASP A:94 , SER A:95 , HOH A:2089 , HOH A:2112 , HOH A:2266BINDING SITE FOR RESIDUE ACT A1300
2AC2SOFTWAREHIS A:88 , TRP A:251 , ASN A:256 , SER A:257 , BMA A:1302 , HOH A:2267 , HOH A:2268 , HOH A:2269 , HOH A:2270 , HOH A:2271BINDING SITE FOR RESIDUE MAN A1301
3AC3SOFTWARETRP A:31 , TYR A:32 , TRP A:61 , GLY A:255 , SER A:257 , MAN A:1301 , BMA A:1303 , HOH A:2272 , HOH A:2273BINDING SITE FOR RESIDUE BMA A1302
4AC4SOFTWARETRP A:31 , ASP A:111 , BMA A:1302BINDING SITE FOR RESIDUE BMA A1303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:251 -Ser A:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WHL)

(-) 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:294
 aligned with Q5YEX6_9BACI | Q5YEX6 from UniProtKB/TrEMBL  Length:493

    Alignment length:296
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
         Q5YEX6_9BACI    35 GFYVDGNTLYDANGQPFVMKGINHGHAWYKDTASTAIPAIAEQGANTIRIVLSDGGQWEKDDIDTVREVIELAEQNKMVAVVEVHDATGRDSRSDLDRAVDYWIEMKDALIGKEDTVIINIANEWYGSWDGAAWADGYIDVIPKLRDAGLTHTLMVDAAGWGQYPQSIHDYGQDVFNADPLKNTIFSIHMYEYAGGDANTVRSNIDRVIDQDLALVIGEFGHRHTDGDVDEDTILSYSEETGTGWLAWSWKGNSAEWDYLDLSEDWAGNHLTDWGNRIVHGANGLQETSKPSTVFT 330
               SCOP domains d2whla_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2whlA00 A:4-299 Glycosidases                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------Cellulase-2whlA01 A:13-257                                                                                                                                                                                                                           ------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eee.........eeeeehhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhhhh....eeeeee.....--..hhhhhhhhhhhhh.eeee......hhhhhhhh..........hhhhhhhhhh..hhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whl A   4 GFSVDGNTLYDANGQPFVMRGINHGHAWYKDTASTAIPAIAEQGANTIRIVLSDGGQWEKDDIDTIREVIELAEQNKMVAVVEVHDATGRDSRSDLNRAVDYWIEMKDALIGKEDTVIINIANEWYGSWDGSAWADGYIDVIPKLRDAGLTHTLMVDAAGWGQYPQSIHDYGQDVFNADPLKNTMFSIHMYEYAGGDANTVRSNIDRVIDQDLALVIGEFGHRHT--DVDEDTILSYSEETGTGWLAWSWKGNSTSWDYLDLSEDWAGQHLTDWGNRIVHGADGLQETSKPSTVFT 299
                                    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      
                                                                                                                                                                                                                                                          228  |                                                                    
                                                                                                                                                                                                                                                             231
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5YEX6_9BACI | Q5YEX6)
molecular function
    GO:0004567    beta-mannosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides.
    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:0016985    mannan endo-1,4-beta-mannosidase activity    Catalysis of the random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q5YEX6_9BACI | Q5YEX6: 2whj
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        Q5YEX6_9BACI | Q5YEX6: 3jug

(-) Related Entries Specified in the PDB File

2whj UNDERSTANDING HOW DIVERSE MANNANASES RECOGNISE HETEROGENEOUS SUBSTRATES
2whk STRUCTURE OF BACILLUS SUBTILIS MANNANASE MAN26
2whm CELLVIBRIO JAPONICUS MAN26A E121A AND E320G DOUBLE MUTANT IN COMPLEX WITH MANNOBIOSE