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(-) Description

Title :  STRUCTURAL BASIS FOR THE PROMISCUOUS SPECIFICITY OF THE CARBOHYDRATE-BINDING MODULES FROM THE BETA-SANDWICH SUPER FAMILY
 
Authors :  S. Najmudin, C. I. P. D. Guerreiro, A. L. Carvalho, D. N. Bolam, J. A. M. Pr M. A. S. Correia, V. D. Alves, L. M. A. Ferreira, M. J. Romao, H. J. Gilber C. M. G. A. Fontes
Date :  26 Sep 05  (Deposition) - 18 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Cellulase Ctcel9D-Cel44A, Pkd Domain, Cbm44, Carbohydrate Binding Module, Beta-Sandwich Proteins, Cellulosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Najmudin, C. I. P. D. Guerreiro, A. L. Carvalho, J. A. M. Prates, M. A. S. Correia, V. D. Alves, L. M. A. Ferreira, M. J. Romao, H. J. Gilbert, D. N. Bolam, C. M. G. A. Fontes
Xyloglucan Is Recognized By Carbohydrate-Binding Modules That Interact With Beta-Glucan Chains.
J. Biol. Chem. V. 281 8815 2006
PubMed-ID: 16314409  |  Reference-DOI: 10.1074/JBC.M510559200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOGLUCANASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: PKD AND CBM44 DOMAINS, 1353-1601
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Other Details: CONTAINS 2 CALCIUM IONS
    Strain: YS
    Synonym: CEL44A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO24Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:4 , GLN A:5 , ASP A:33 , ASP A:35 , ASP A:76 , HOH A:2171BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREASP A:96 , ASN A:101 , GLU A:103 , LYS A:130 , ARG A:133 , ASP A:245BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREILE A:73 , SER A:81 , SER A:82 , SER A:190 , GLU A:191 , HOH A:2159 , HOH A:2368 , HOH A:2369BINDING SITE FOR RESIDUE EDO A 401
04AC4SOFTWAREPHE A:100 , ASN A:101 , PHE A:102 , ASP A:104BINDING SITE FOR RESIDUE EDO A 402
05AC5SOFTWAREILE A:10 , GLY A:48 , TYR A:49 , GLU A:50 , TRP A:189 , HOH A:2371BINDING SITE FOR RESIDUE EDO A 403
06AC6SOFTWAREGLN A:5 , SER A:53 , THR A:54 , THR A:55 , THR A:57 , HOH A:2372BINDING SITE FOR RESIDUE EDO A 404
07AC7SOFTWAREGLN A:5 , ALA A:6 , GLU A:50 , HOH A:2381BINDING SITE FOR RESIDUE EDO A 405
08AC8SOFTWARELYS A:8 , ASP A:47 , LYS A:61 , TYR A:62 , LYS A:63 , THR A:115 , EDO A:409 , HOH A:2373BINDING SITE FOR RESIDUE EDO A 406
09AC9SOFTWARETHR A:12 , ASN A:27 , SER A:29BINDING SITE FOR RESIDUE EDO A 407
10BC1SOFTWAREALA A:39 , TYR A:40 , TYR A:41 , THR A:52 , SER A:53 , THR A:54 , HOH A:2375BINDING SITE FOR RESIDUE EDO A 408
11BC2SOFTWAREASP A:21 , ILE A:32 , LYS A:61 , EDO A:406 , HOH A:2094 , HOH A:2376 , HOH A:2377BINDING SITE FOR RESIDUE EDO A 409
12BC3SOFTWAREASP A:44 , GLY A:46 , LYS A:69 , LYS A:71 , HOH A:2378 , HOH A:2380BINDING SITE FOR RESIDUE EDO A 410
13BC4SOFTWAREPRO A:7 , LYS A:8 , ALA A:9 , SER A:82 , SER A:83 , TRP A:189 , SER A:190 , VAL A:192 , HOH A:2381 , HOH A:2382BINDING SITE FOR RESIDUE EDO A 411
14BC5SOFTWARELEU A:107 , THR A:112 , VAL A:120 , VAL A:121 , ASP A:219 , HOH A:2217BINDING SITE FOR RESIDUE EDO A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C26)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:14 -Pro A:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C26)

(-) Exons   (0, 0)

(no "Exon" information available for 2C26)

(-) 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:250
 aligned with A3DD30_CLOTH | A3DD30 from UniProtKB/TrEMBL  Length:1601

    Alignment length:250
                                                                                                                                                                                                                                                                                1601  
                                  1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593       | -
        A3DD30_CLOTH   1354 PENQAPKAIFTFSPEDPVTDENVVFNASNSIDEDGTIAYYVWDFGDGYEGTSTTPTITYKYKNPGTYKVKLIVTDNQGASSSFTATIKVTSATGDNSKFNFEDGTLGGFTTSGTNATGVVVNTTEKAFKGERGLKWTVTSEGEGTAELKLDGGTIVVPGTTMTFRIWIPSGAPIAAIQPYIMPHTPDWSEVLWNSTWKGYTMVKTDDWNEITLTLPEDVDPTWPQQMGIQVQTIDEGEFTIYVDAIDW--    -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.........eeee..........eeeeeee.....eeee...eeee.....eeeeeeeeeee....eeeeeeeeee....................eeeeeeeeeeeeee.........eeeeeeeeeeeeeeeeeee.........eeeeeeee.....eeeeeeeeee.................hhh...eeeeeeee..........eeeeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2c26 A    2 PENQAPKAIFTFSPEDPVTDENVVFNASNSIDEDGTIAYYVWDFGDGYEGTSTTPTITYKYKNPGTYKVKLIVTDNQGASSSFTATIKVTSATGDNSKFNFEDGTLGGFTTSGTNATGVVVNTTEKAFKGERGLKWTVTSEGEGTAELKLDGGTIVVPGTTMTFRIWIPSGAPIAAIQPYIMPHTPDWSEVLWNSTWKGYTMVKTDDWNEITLTLPEDVDPTWPQQMGIQVQTIDEGEFTIYVDAIDWLE  251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251


Chain A from PDB  Type:PROTEIN  Length:250
 aligned with P71140_CLOTM | P71140 from UniProtKB/TrEMBL  Length:1601

    Alignment length:250
                                                                                                                                                                                                                                                                                1601  
                                  1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593       | -
        P71140_CLOTM   1354 PENQAPKAIFTFSPEDPVTDENVVFNASNSIDEDGTIAYYAWDFGDGYEGTSTTPTITYKYKNPGTYKVKLIVTDNQGASSSFTATIKVTSATGDNSKFNFEDGTLGGFTTSGTNATGVVVNTTEKAFKGERGLKWTVTSEGEGTAELKLDGGTIVVPGTTMTFRIWIPSGAPIAAIQPYIMPHTPDWSEVLWNSTWKGYTMVKTDDWNEITLTLPEDVDPTWPQQMGIQVQTIDEGEFTIYVDAIDW--    -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.........eeee..........eeeeeee.....eeee...eeee.....eeeeeeeeeee....eeeeeeeeee....................eeeeeeeeeeeeee.........eeeeeeeeeeeeeeeeeee.........eeeeeeee.....eeeeeeeeee.................hhh...eeeeeeee..........eeeeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2c26 A    2 PENQAPKAIFTFSPEDPVTDENVVFNASNSIDEDGTIAYYVWDFGDGYEGTSTTPTITYKYKNPGTYKVKLIVTDNQGASSSFTATIKVTSATGDNSKFNFEDGTLGGFTTSGTNATGVVVNTTEKAFKGERGLKWTVTSEGEGTAELKLDGGTIVVPGTTMTFRIWIPSGAPIAAIQPYIMPHTPDWSEVLWNSTWKGYTMVKTDDWNEITLTLPEDVDPTWPQQMGIQVQTIDEGEFTIYVDAIDWLE  251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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  (0, 0)

(no "SCOP Domain" information available for 2C26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C26)

(-) Gene Ontology  (7, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (A3DD30_CLOTH | A3DD30)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    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: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:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Chain A   (P71140_CLOTM | P71140)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    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:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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  2c26
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  P71140_CLOTM | P71140
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 Related Entries

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

UniProtKB/Swiss-Prot
        P71140_CLOTM | P71140: 1wmx 2e0p 2eex 2ej1 2eqd
UniProtKB/TrEMBL
        A3DD30_CLOTH | A3DD30: 1wmx 1wzx 2e0p 2eex 2ej1 2eqd
        P71140_CLOTM | P71140: 2c24 2c4x 2e4t 2eo7

(-) Related Entries Specified in the PDB File

1wmx CRYSTAL STRUCTURE OF FAMILY 30 CARBOHYDRATE BINDING MODULE
1wzx CRYSTAL STRUCTURE OF FAMILY 30 CARBOHYDRATE BINDING MODULE.
2c24 FAMILY 30 CARBOHYDRATE-BINDING MODULE OF CELLULOSOMAL CELLULASE CEL9D-CEL44B OF CLOSTRIDIUM THERMOCELLUM