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(-) Description

Title :  CRYSTAL STRUCTURE OF ALKALINE MANNANASE FROM BACILLUS SP. STRAIN JAMB-602: CATALYTIC DOMAIN AND ITS CARBOHYDRATE BINDING MODULE
 
Authors :  M. Akita, N. Takeda, K. Hirasawa, H. Sakai, M. Kawamoto, M. Yamamoto, W. Y. Hatada, S. Ito, K. Horikoshi
Date :  15 Jun 04  (Deposition) - 15 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Catalytic Domain, Cbm, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Akita, N. Takeda, K. Hirasawa, H. Sakai, M. Kawamoto, M. Yamamoto, W. D. Grant, Y. Hatada, S. Ito, K. Horikoshi
Crystallization And Preliminary X-Ray Study Of Alkaline Mannanase From An Alkaliphilic Bacillus Isolate.
Acta Crystallogr. , Sect. D V. 60 1490 2004
PubMed-ID: 15272186  |  Reference-DOI: 10.1107/S0907444904014313

(-) Compounds

Molecule 1 - ENDO-BETA-1,4-MANNANASE
    Chains: A
    EC Number: 3.2.1.78
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PHSP64
    Expression System Strain: ISW1214
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, CARBOHYDRATE BINDING MODULE
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 244966
    Strain: JAMB-602

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:243 , ARG A:275 , ASN A:298 , ASP A:299 , ASN A:304BINDING SITE FOR RESIDUE CL A 501
2AC2SOFTWAREARG A:275 , LYS A:285BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREASP A:345 , GLU A:347 , LYS A:371 , HIS A:374 , ASP A:485BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWAREHIS A:256 , ASP A:262 , VAL A:263 , GLU A:265 , HOH A:645 , HOH A:730BINDING SITE FOR RESIDUE NA A 504
5AC5SOFTWAREGLU A:158 , GLU A:253 , HOH A:678 , HOH A:687 , HOH A:824 , HOH A:854BINDING SITE FOR RESIDUE NA A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WKY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:282 -Ser A:283
2Gly A:361 -Pro A:362

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WKY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WKY)

(-) Exons   (0, 0)

(no "Exon" information available for 1WKY)

(-) 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:446
 aligned with Q4W8M3_9BACI | Q4W8M3 from UniProtKB/TrEMBL  Length:490

    Alignment length:464
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486    
         Q4W8M3_9BACI    27 TSTANANSGFYVSGTTLYDANGNPFVMRGINHGHAWYKDQATTAIEGIANTGANTVRIVLSDGGQWTKDDIQTVRNLISLAEDNNLVAVLEVHDATGYDSIASLNRAVDYWIEMRSALIGKEDTVIINIANEWFGSWDGAAWADGYKQAIPRLRNAGLNNTLMIDAAGWGQFPQSIHDYGREVFNADPQRNTMFSIHMYEYAGGNASQVRTNIDRVLNQDLALVIGEFGHRHTNGDVDESTIMSYSEQRGVGWLAWSWKGNGPEWEYLDLSNDWAGNNLTAWGNTIVNGPYGLRETSKLSTVFTGGGSDGRTSPTTLYDFEESTQGWTGSSLSRGPWTVTEWSSKGNHSLKADIQMSSNSQHYLHVIQNRSLQQNSRIQATVKHANWGSVGNGMTARLYVKTGHGYTWYSGSFVPINGSSGTTLSLDLSNVQNLSQVREIGVQFQSESNSSGQTSIYIDNVIVE 490
               SCOP domains -----  d1wkya2 A:34-330 Beta-mannanase                                                                                                                                                                                                                                                                                   d1wkya1 A:340-490 Endo-beta-1,4-mannanase C-terminal domain                                                                                             SCOP domains
               CATH domains 1wkyA  01 A:27-330 Glycosidases                                                                                                                                                                                                                                                                                          ------------------------------------------------------------------------       ------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------Cellulase-1wkyA01 A:44-288                                                                                                                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--...eee..eee.........eeeeehhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhhh......eeee.........hhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhhhh....eeeeee..ee..ee.hhhhhhhhhhhh..eeee......hhhhhhhh..........hhhhhhhhhh..hhhhhh.......---------.eeee........eeee...eeeeee.........eeeeeeee....eeeeeeeeee......eeeeeeee.-------.eeeeeeeee....eeee...eee.....eeeeee.....hhh.eeeeeeeeee.....eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wky A  27 GRPAN--SGFYVSGTTLYDANGNPFVMRGINHGHAWYKDQATTAIEGIANTGANTVRIVLSDGGQWTKDDIQTVRNLISLAEDNNLVAVLEVHDATGYDSIASLNRAVDYWIEMRSALIGKEDTVIINIANEWFGSWDGAAWADGYKQAIPRLRNAGLNNTLMIDAAGWGQFPQSIHDYGREVFNADPQRNTMFSIHMYEYAGGNASQVRTNIDRVLNQDLALVIGEFGHRHTNGDVDESTIMSYSEQRGVGWLAWSWKGNGPEWEYLDLSNDWAGNNLTAWGNTIVNGPYGLRETSKLSTVFT---------PTTLYDFEESTQGWTGSSLSRGPWTVTEWSSKGNHSLKADIQMSSNSQHYLHVIQNRSLQQNSRIQATVKHA-------GMTARLYVKTGHGYTWYSGSFVPINGSSGTTLSLDLSNVQNLSQVREIGVQFQSESNSSGQTSIYIDNVIVE 490
                                |  |36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   |     -   |   346       356       366       376       386       396       406    |    -  |    426       436       446       456       466       476       486    
                               31 34                                                                                                                                                                                                                                                                                                     330       340                                                                    411     419
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
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  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4W8M3_9BACI | Q4W8M3)
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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