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(-) Description

Title :  CARBOHYDRATE BINDING MODULE (CBM6CM-2) FROM CELLVIBRIO MIXTUS LICHENASE 5A IN COMPLEX WITH CELLOBIOSE
 
Authors :  M. Czjzek, V. M. R. Pires, J. Henshaw, J. A. M. Prates, D. Bolam, B. Henrissat, H. J. Gilbert
Date :  03 Mar 04  (Deposition) - 11 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbohydrate Binding Module, Cbm6, Mixted Beta1, 3-1, 4 Linked Glucan, Cellobiose (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. M. R. Pires, J. Henshaw, J. A. M. Prates, D. Bolam, L. M. A. Ferreira, C. M. G. A. Fontes, B. Henrissat, A. Planas, H. J. Gilbert, M. Czjzek
The Crystal Structure Of The Family 6 Carbohydrate Binding Module From Cellvibrio Mixtus Endoglucanase 5A In Complex With Oligosaccharides Reveals Two Distinct Binding Sites With Different Ligand Specificities
J. Biol. Chem. V. 279 21560 2004
PubMed-ID: 15010454  |  Reference-DOI: 10.1074/JBC.M401599200

(-) Compounds

Molecule 1 - CELLULASE B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCARBOHYDRATE BINDING MODULE, RESIDUES 493-622
    Organism ScientificCELLVIBRIO MIXTUS
    Organism Taxid39650

 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, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2CA4Ligand/IonCALCIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1BGC4Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:39 , GLU A:73 , GLU A:74 , ALA A:75 , GLY A:76 , GLY A:77 , BGC A:1132 , HOH A:2165 , HOH A:2166 , HOH A:2167 , HOH A:2168BINDING SITE FOR RESIDUE BGC A1131
02AC2SOFTWAREGLN A:13 , TRP A:39 , SER A:41 , ALA A:43 , ALA A:75 , GLY A:76 , BGC A:1131 , HOH A:2023 , HOH A:2025 , HOH A:2169 , HOH A:2170 , ASN B:48BINDING SITE FOR RESIDUE BGC A1132
03AC3SOFTWARETRP B:39 , GLU B:73 , GLU B:74 , ALA B:75 , GLY B:76 , LYS B:114 , BGC B:1132 , HOH B:2158BINDING SITE FOR RESIDUE BGC B1131
04AC4SOFTWAREASN A:48 , GLN B:13 , TRP B:39 , SER B:41 , ALA B:75 , GLY B:76 , BGC B:1131 , HOH B:2160BINDING SITE FOR RESIDUE BGC B1132
05AC5SOFTWAREGLU A:9 , ASP A:10 , GLN A:19 , TYR B:33 , TRP B:92 , BGC B:1134 , HOH B:2161 , HOH B:2164 , HOH B:2165 , HOH B:2166 , HOH B:2170BINDING SITE FOR RESIDUE BGC B1133
06AC6SOFTWAREGLU B:20 , GLY B:32 , TYR B:33 , TRP B:92 , ASN B:121 , BGC B:1133 , HOH B:2162 , HOH B:2163 , HOH B:2167 , HOH B:2168 , HOH B:2170BINDING SITE FOR RESIDUE BGC B1134
07AC7SOFTWAREGLN A:7 , GLU A:9 , LYS A:29 , ASN A:123 , HOH A:2010BINDING SITE FOR RESIDUE CA A1133
08AC8SOFTWAREGLY A:16 , TYR A:33 , ASP A:35 , ASP A:38 , HOH A:2069 , HOH A:2075BINDING SITE FOR RESIDUE CA A1134
09AC9SOFTWAREGLY B:16 , TYR B:33 , ASP B:35 , ASP B:38 , HOH B:2068BINDING SITE FOR RESIDUE CA B1135
10BC1SOFTWAREGLN B:7 , GLU B:9 , LYS B:29 , ASN B:123 , HOH B:2014BINDING SITE FOR RESIDUE CA B1136

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:78 -Pro A:79
2Ala B:78 -Pro B:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UYX)

(-) 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:130
 aligned with O07653_9GAMM | O07653 from UniProtKB/TrEMBL  Length:622

    Alignment length:130
                                   501       511       521       531       541       551       561       571       581       591       601       611       621
         O07653_9GAMM   492 TVIATIQAEDHSQQSGTQQETTTDTGGGKNVGYIDAGDWLSYAGTPVNIPSSGSYLIEYRVASQNGGGSLTFEEAGGAPVHGTIAIPATGGWQTWTTIQHTVNLSAGSHQFGIKANAGGWNLNWIRINKT 621
               SCOP domains d1uyxa_ A: Cellulase B (lichenase 5a)                                                                                              SCOP domains
               CATH domains 1uyxA00 A:1-130 Galactose-binding domain-like                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eee..eeee.......eeee......eee.....eee...eeeeeeeeee.....eeeeeee.....eeeeeee........eeeeeeeeee..eee.eeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uyx A   1 MVIATIQAEDHSQQSGTQQETTTDTGGGKNVGYIDAGDWLSYAGTPVNIPSSGSYLIEYRVASQNGGGSLTFEEAGGAPVHGTIAIPATGGWQTWTTIQHTVNLSAGSHQFGIKANAGGWNLNWIRINKT 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with O07653_9GAMM | O07653 from UniProtKB/TrEMBL  Length:622

    Alignment length:130
                                   501       511       521       531       541       551       561       571       581       591       601       611       621
         O07653_9GAMM   492 TVIATIQAEDHSQQSGTQQETTTDTGGGKNVGYIDAGDWLSYAGTPVNIPSSGSYLIEYRVASQNGGGSLTFEEAGGAPVHGTIAIPATGGWQTWTTIQHTVNLSAGSHQFGIKANAGGWNLNWIRINKT 621
               SCOP domains d1uyxb_ B: Cellulase B (lichenase 5a)                                                                                              SCOP domains
               CATH domains 1uyxB00 B:1-130 Galactose-binding domain-like                                                                                      CATH domains
           Pfam domains (1) ------CBM_6-1uyxB01 B:7-129                                                                                                      - Pfam domains (1)
           Pfam domains (2) ------CBM_6-1uyxB02 B:7-129                                                                                                      - Pfam domains (2)
         Sec.struct. author .eeeeee.....eee..eeee.......eeee......eee.....eee...eeeeeeeeee.....eeeeeee.....eeeeeee.........eeeeeeeee..eee.eeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uyx B   1 MVIATIQAEDHSQQSGTQQETTTDTGGGKNVGYIDAGDWLSYAGTPVNIPSSGSYLIEYRVASQNGGGSLTFEEAGGAPVHGTIAIPATGGWQTWTTIQHTVNLSAGSHQFGIKANAGGWNLNWIRINKT 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O07653_9GAMM | O07653)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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

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

UniProtKB/TrEMBL
        O07653_9GAMM | O076531uxz 1uy0 1uyy 1uyz 1uz0

(-) Related Entries Specified in the PDB File

1uxz CARBOHYDRATE BINDING MODULE (CBM6CM-2) FROM CELLVIBRIO MIXTUS LICHENASE 5A
1uy0 CARBOHYDRATE BINDING MODULE (CBM6CM-2) FROM CELLVIBRIO MIXTUS LICHENASE 5A IN COMPLEX WITH GLC-1,3-GLC-1,4-GLC-1,3-GLC
1uyy CARBOHYDRATE BINDING MODULE (CBM6CM-2) FROM CELLVIBRIO MIXTUS LICHENASE 5A IN COMPLEX WITH CELLOTRIOSE
1uyz CARBOHYDRATE BINDING MODULE (CBM6CM-2) FROM CELLVIBRIO MIXTUS LICHENASE 5A IN COMPLEX WITH XYLOTETRAOSE
1uz0 CARBOHYDRATE BINDING MODULE (CBM6CM-2) FROM CELLVIBRIO MIXTUS LICHENASE 5A IN COMPLEX WITH GLC-4GLC-3GLC-4GLC