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(-) Description

Title :  STRUCTURAL AND THERMODYNAMIC DISSECTION OF SPECIFIC MANNAN RECOGNITION BY A CARBOHYDRATE-BINDING MODULE, TMCBM27
 
Authors :  A. B. Boraston, T. J. Revett, C. M. Boraston, D. Nurizzo, G. J. Davies
Date :  07 Apr 03  (Deposition) - 17 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase/Carbohydrate Binding, Mannan Binding, Carbohydrate Binding Module, Polysaccharide Degradation, Tmcbm27, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Boraston, T. J. Revett, C. M. Boraston, D. Nurizzo, G. J. Davies
Structural And Thermodynamic Dissection Of Specific Mannan Recognition By A Carbohydrate Binding Module, Tmcbm27
Structure V. 11 665 2003
PubMed-ID: 12791255  |  Reference-DOI: 10.1016/S0969-2126(03)00100-X

(-) Compounds

Molecule 1 - BETA-MANNOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28-TMCBM27
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET 28
    Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 505-680
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: TMCBM27

 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , GLY A:44 , GLY A:46 , ASP A:165 , HOH A:2056 , HOH A:2148BINDING SITE FOR RESIDUE CA A1174
2AC2SOFTWAREASP B:12 , GLY B:44 , GLY B:46 , ASP B:165 , HOH B:2048 , HOH B:2127BINDING SITE FOR RESIDUE CA B1174

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OF3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:34 -Pro A:35
2Asn A:101 -Pro A:102
3Ser B:34 -Pro B:35
4Asn B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OF3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OF3)

(-) Exons   (0, 0)

(no "Exon" information available for 1OF3)

(-) 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:176
 aligned with Q9RIK9_THEMT | Q9RIK9 from UniProtKB/TrEMBL  Length:680

    Alignment length:176
                                   511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671      
         Q9RIK9_THEMT   502 KVVNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVGNGALQLNVKLPGKSDWEEVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPGWVKIGLDMNNANVESAEIITFGGKEYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIFIDNVRLYKRT 677
               SCOP domains d1of3a_ A: Beta-mannosidase, C-terminal domain                                                                                                                                   SCOP domains
               CATH domains -1of3A00 A:-1-173 Galactose-binding domain-like                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee...hhhhhh.eeeeeee..eeeeeeeeee.hhhhheeeeeeee......eeeeeeee..hhhhh.eeeeeeeee.......ee..eeeee...eee......ee.hhheeeee..eeeeeeeeeee........eeeeeeeee...eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1of3 A  -2 mASNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVGNGALQLNVKLPGKSDWEEVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPGWVKIGLDmNNANVESAEIITFGGKEYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIFIDNVRLYKRT 173
                            |        7        17        27        37        47        57        67        77        87        97       107   |   117       127       137       147       157       167      
                            |                                                                                                              111-MSE                                                          
                           -2-MSE                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with Q9RIK9_THEMT | Q9RIK9 from UniProtKB/TrEMBL  Length:680

    Alignment length:174
                                   513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673    
         Q9RIK9_THEMT   504 VNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVGNGALQLNVKLPGKSDWEEVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPGWVKIGLDMNNANVESAEIITFGGKEYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIFIDNVRLYKRT 677
               SCOP domains d1of3b_ B: Beta-mannosidase, C-terminal domain                                                                                                                                 SCOP domains
               CATH domains 1of3B00 B:0-173 Galactose-binding domain-like                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee...hhhhhh.eeeeeee..eeeeeeeeee.hhhhheeeeeeee......eeeeeeee..hhhhh.eeeeeeeee...............................hhheeeee..eeeeeeeeeee........eeeeeeeee...eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1of3 B   0 SNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVGNGALQLNVKLPGKSDWEEVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPGWVKIGLDmNNANVESAEIITFGGKEYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIFIDNVRLYKRT 173
                                     9        19        29        39        49        59        69        79        89        99       109 |     119       129       139       149       159       169    
                                                                                                                                         111-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OF3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9RIK9_THEMT | Q9RIK9)
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 Specified in the PDB File

1of4 STRUCTURAL AND THERMODYNAMIC DISSECTION OF SPECIFIC MANNAN RECOGNITION BY A CARBOHYDRATE -BINDING MODULE, TMCBM27