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(-) Description

Title :  ATOMIC RESOLUTION STRUCTURE OF AN INVERTING GLYCOSIDASE IN COMPLEX WITH SUBSTRATE
 
Authors :  D. M. A. Guerin, M. -B. Lascombe, M. Costabel, H. Souchon, V. Lamzin, P. Beguin, P. M. Alzari
Date :  29 Jan 02  (Deposition) - 13 Mar 02  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Inverting Glycosidase, Atomic Resolution, Protein-Carbohydrate Interactions, Reaction Mechanism, Cellulase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Guerin, M. B. Lascombe, M. Costabel, H. Souchon, V. Lamzin, P. Beguin, P. M. Alzari
Atomic (0. 94 A) Resolution Structure Of An Inverting Glycosidase In Complex With Substrate.
J. Mol. Biol. V. 316 1061 2002
PubMed-ID: 11884144  |  Reference-DOI: 10.1006/JMBI.2001.5404
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOGLUCANASE A
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCT128
    Expression System Strain: NCIB 10682
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC CORE (RESIDUES 33-395)
    Gene: CELA
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: ENDOGLUCANASE CELA, EGA, CELLULASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1BGC8Ligand/IonBETA-D-GLUCOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:79 , GLY A:145 , GLY A:148 , ARG A:204 , TRP A:205 , BGC A:402 , HOH A:523 , HOH A:825BINDING SITE FOR RESIDUE BGC A 401
2AC2SOFTWARETRP A:132 , ALA A:149 , ALA A:150 , PRO A:201 , TRP A:205 , BGC A:401 , BGC A:403 , HOH A:537 , HOH A:654 , HOH A:696 , HOH A:724 , HOH A:741BINDING SITE FOR RESIDUE BGC A 402
3AC3SOFTWAREARG A:84 , VAL A:93 , GLN A:95 , TRP A:132 , ALA A:150 , ASP A:152 , TYR A:215 , ARG A:281 , BGC A:402 , BGC A:404 , HOH A:508 , HOH A:724 , HOH A:851 , HOH A:942BINDING SITE FOR RESIDUE BGC A 403
4AC4SOFTWAREARG A:84 , GLN A:95 , TYR A:277 , ASP A:278 , TYR A:372 , BGC A:403 , BGC A:405 , HOH A:651 , HOH A:913BINDING SITE FOR RESIDUE BGC A 404
5AC5SOFTWARETYR A:277 , BGC A:404 , HOH A:544 , HOH A:650 , HOH A:653 , HOH A:688 , HOH A:912 , HOH A:913BINDING SITE FOR RESIDUE BGC A 405
6AC6SOFTWAREARG A:84 , GLN A:95 , ASP A:278 , TYR A:371 , TYR A:372 , BGC A:407 , HOH A:651 , HOH A:913BINDING SITE FOR RESIDUE BGC A 406
7AC7SOFTWARETYR A:277 , TYR A:369 , TYR A:372 , BGC A:406 , BGC A:408 , HOH A:650 , HOH A:651 , HOH A:676 , HOH A:688 , HOH A:912BINDING SITE FOR RESIDUE BGC A 407
8AC8SOFTWARETYR A:277 , ASN A:331 , ASN A:333 , TYR A:369 , BGC A:407 , HOH A:664 , HOH A:676 , HOH A:779BINDING SITE FOR RESIDUE BGC A 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:35 -Pro A:36

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F8PS00812 Glycosyl hydrolases family 8 signature.GUNA_CLOTH150-168  1A:150-168

(-) Exons   (0, 0)

(no "Exon" information available for 1KWF)

(-) 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:363
 aligned with GUNA_CLOTH | A3DC29 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:363
                                    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       312       322       332       342       352       362       372       382       392   
           GUNA_CLOTH    33 AGVPFNTKYPYGPTSIADNQSEVTAMLKAEWEDWKSKRITSNGAGGYKRVQRDASTNYDTVSEGMGYGLLLAVCFNEQALFDDLYRYVKSHFNGNGLMHWHIDANNNVTSHDGGDGAATDADEDIALALIFADKLWGSSGAINYGQEARTLINNLYNHCVEHGSYVLKPGDRWGGSSVTNPSYFAPAWYKVYAQYTGDTRWNQVADKCYQIVEEVKKYNNGTGLVPDWCTASGTPASGQSYDYKYDATRYGWRTAVDYSWFGDQRAKANCDMLTKFFARDGAKGIVDGYTIQGSKISNNHNASFIGPVAAASMTGYDLNFAKELYRETVAVKDSEYYGYYGNSLRLLTLLYITGNFPNPLSDL 395
               SCOP domains d1kwfa_ A: CelA cellulase                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kwfA00 A:33-395  [code=1.50.10.10, no name defined]                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -Glyco_hydro_8-1kwfA01 A:34-386                                                                                                                                                                                                                                                                                                                                   --------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhee........ee..hhhhh..eehhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........ee...............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F8 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kwf A  33 AGVPFNTKYPYGPTSIADNQSEVTAMLKAEWEDWKSKRITSNGAGGYKRVQRDASTNYDTVSQGMGYGLLLAVCFNEQALFDDLYRYVKSHFNGNGLMHWHIDANNNVTSHDGGDGAATDADEDIALALIFADKLWGSSGAINYGQEARTLINNLYNHCVEHGSYVLKPGDRWGGSSVTNPSYFAPAWYKVYAQYTGDTRWNQVADKCYQIVEEVKKYNNGTGLVPDWCTASGTPASGQSYDYKYDATRYGWRTAVDYSWFGDQRAKANCDMLTKFFARDGAKGIVDGYTIQGSKISNNHNASFIGPVAAASMTGYDLNFAKELYRETVAVKDSEYYGYYGNSLRLLTLLYITGNFPNPLSDL 395
                                    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       312       322       332       342       352       362       372       382       392   


Chain A from PDB  Type:PROTEIN  Length:363
 aligned with GUNA_CLOTM | P0C2S2 from UniProtKB/Swiss-Prot  Length:14

    Alignment length:363
                                        14                                                                                                                                                                                                                                                                                                                                                             
                                    10   |     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   
           GUNA_CLOTM     1 AGVPFNTKTPYGPT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1kwfa_ A: CelA cellulase                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kwfA00 A:33-395  [code=1.50.10.10, no name defined]                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -Glyco_hydro_8-1kwfA01 A:34-386                                                                                                                                                                                                                                                                                                                                   --------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhee........ee..hhhhh..eehhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........ee...............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kwf A  33 AGVPFNTKYPYGPTSIADNQSEVTAMLKAEWEDWKSKRITSNGAGGYKRVQRDASTNYDTVSQGMGYGLLLAVCFNEQALFDDLYRYVKSHFNGNGLMHWHIDANNNVTSHDGGDGAATDADEDIALALIFADKLWGSSGAINYGQEARTLINNLYNHCVEHGSYVLKPGDRWGGSSVTNPSYFAPAWYKVYAQYTGDTRWNQVADKCYQIVEEVKKYNNGTGLVPDWCTASGTPASGQSYDYKYDATRYGWRTAVDYSWFGDQRAKANCDMLTKFFARDGAKGIVDGYTIQGSKISNNHNASFIGPVAAASMTGYDLNFAKELYRETVAVKDSEYYGYYGNSLRLLTLLYITGNFPNPLSDL 395
                                    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       312       322       332       342       352       362       372       382       392
   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: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (9, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GUNA_CLOTM | P0C2S2)
molecular function
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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.
    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   (GUNA_CLOTH | A3DC29)
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: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.
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        GUNA_CLOTH | A3DC29: 1cem 1is9
        GUNA_CLOTM | P0C2S2: 1cem 1is9

(-) Related Entries Specified in the PDB File

1cem 1CEM CONTAINS THE WILD-TYPE ENZYME REFINED AT 1.65 ANGSTROMS.