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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) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
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 35-341
    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, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:93 , ASP A:94 , SER A:95 , ASP A:98 , HOH A:2142 , HOH A:2375 , HOH A:2376 , HOH A:2377BINDING SITE FOR RESIDUE GOL A1311
2AC2SOFTWAREASP A:133 , GLY A:134 , SER A:135 , TYR A:174 , HOH A:2226BINDING SITE FOR RESIDUE ACT A1312
3AC3SOFTWAREARG A:96 , SER A:97 , HOH A:2378BINDING SITE FOR RESIDUE ACT A1313
4AC4SOFTWARETRP A:61 , ASP A:268 , HOH A:2091 , HOH A:2370 , HOH A:2373BINDING SITE FOR RESIDUE NA A1318
5AC5SOFTWAREHIS A:225 , GLU A:234 , ARG A:280BINDING SITE FOR RESIDUE ACT A1314
6AC6SOFTWAREARG A:96 , ASP A:139 , HOH A:2197BINDING SITE FOR RESIDUE ACT A1315
7AC7SOFTWARESER A:257 , THR A:258 , PRO A:309 , THR A:310 , HOH A:2374 , HOH A:2379BINDING SITE FOR RESIDUE GOL A1316
8AC8SOFTWAREASP A:150 , PRO A:183 , ARG A:280 , GLY A:284 , ALA A:285 , HOH A:2380BINDING SITE FOR RESIDUE ACT A1317

(-) SS Bonds  (0, 0)

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

(-) 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 2WHJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WHJ)

(-) 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:308
 aligned with MAN5_BACAG | G1K3N4 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
           MAN5_BACAG     1 AGFYVDGNTLYDANGQPFVMRGINHGHAWYKDTASTAIPAIAEQGANTIRIVLSDGGQWEKDDIDTIREVIELAEQNKMVAVVEVHDATGRDSRSDLNRAVDYWIEMKDALIGKEDTVIINIANEWYGSWDGSAWADGYIDVIPKLRDAGLTHTLMVDAAGWGQYPQSIHDYGQDVFNADPLKNTMFSIHMYEYAGGDANTVRSNIDRVIDQDLALVIGEFGHRHTDGDVDEDTILSYSEETGTGWLAWSWKGNSTEWDYLDLSEDWAGQHLTDWGNRIVHGADGLQETSKPSTVFTDDNGGHPEPPT 308
               SCOP domains d2whja_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2whjA00 A:3-310 Glycosidases                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------Cellulase-2whjA01 A:13-257                                                                                                                                                                                                                           ----------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.........eeeeehhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhh.eeee......hhhhhhhh..........hhhhhhhhhh..hhhhhh..hhhhh.hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whj A   3 AGFYVDGNTLYDANGQPFVMRGINHGHAWYKDTASTAIPAIAEQGANTIRIVLSDGGQWEKDDIDTIREVIELAEQNKMVAVVEVHDATGRDSRSDLNRAVDYWIEMKDALIGKEDTVIINIANEWYGSWDGSAWADGYIDVIPKLRDAGLTHTLMVDAAGWGQYPQSIHDYGQDVFNADPLKNTMFSIHMYEYAGGDANTVRSNIDRVIDQDLALVIGEFGHRHTDGDVDEDTILSYSEETGTGWLAWSWKGNSTEWDYLDLSEDWAGQHLTDWGNRIVHGADGLQETSKPSTVFTDDNGGHPEPPT 310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        


Chain A from PDB  Type:PROTEIN  Length:308
 aligned with Q5YEX6_9BACI | Q5YEX6 from UniProtKB/TrEMBL  Length:493

    Alignment length:308
                                    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        
         Q5YEX6_9BACI    34 SGFYVDGNTLYDANGQPFVMKGINHGHAWYKDTASTAIPAIAEQGANTIRIVLSDGGQWEKDDIDTVREVIELAEQNKMVAVVEVHDATGRDSRSDLDRAVDYWIEMKDALIGKEDTVIINIANEWYGSWDGAAWADGYIDVIPKLRDAGLTHTLMVDAAGWGQYPQSIHDYGQDVFNADPLKNTIFSIHMYEYAGGDANTVRSNIDRVIDQDLALVIGEFGHRHTDGDVDEDTILSYSEETGTGWLAWSWKGNSAEWDYLDLSEDWAGNHLTDWGNRIVHGANGLQETSKPSTVFTDDNGGAPEPPT 341
               SCOP domains d2whja_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2whjA00 A:3-310 Glycosidases                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------Cellulase-2whjA01 A:13-257                                                                                                                                                                                                                           ----------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.........eeeeehhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeee..........hhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhh.eeee......hhhhhhhh..........hhhhhhhhhh..hhhhhh..hhhhh.hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whj A   3 AGFYVDGNTLYDANGQPFVMRGINHGHAWYKDTASTAIPAIAEQGANTIRIVLSDGGQWEKDDIDTIREVIELAEQNKMVAVVEVHDATGRDSRSDLNRAVDYWIEMKDALIGKEDTVIINIANEWYGSWDGSAWADGYIDVIPKLRDAGLTHTLMVDAAGWGQYPQSIHDYGQDVFNADPLKNTMFSIHMYEYAGGDANTVRSNIDRVIDQDLALVIGEFGHRHTDGDVDEDTILSYSEETGTGWLAWSWKGNSTEWDYLDLSEDWAGQHLTDWGNRIVHGADGLQETSKPSTVFTDDNGGHPEPPT 310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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, 15)

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.

Chain A   (MAN5_BACAG | G1K3N4)
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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5YEX6_9BACI | Q5YEX6: 2whl 3jug

(-) Related Entries Specified in the PDB File

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