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(-) Description

Title :  ENDOGLUCANASE CEL5A IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-CELLOBIOSIDE AT 1.15 A RESOLUTION
 
Authors :  A. Varrot, G. J. Davies
Date :  09 Aug 02  (Deposition) - 15 Aug 02  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycosidase, Endoglucanase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Varrot, G. J. Davies
Direct Experimental Observation Of The Hydrogen-Bonding Network Of A Glycosidase Along Its Reaction Coordinate Revealed By Atomic Resolution Analyses Of Endoglucanase Cel5A
Acta Crystallogr. , Sect. D V. 59 447 2003
PubMed-ID: 12595701  |  Reference-DOI: 10.1107/S0907444902023405

(-) Compounds

Molecule 1 - ENDOGLUCANASE 5A
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: THERMAMYL-AMYLASE PROMOTOR
    Expression System Strain: PL2306
    Expression System Taxid: 1423
    Expression System Vector: PMOL995
    Fragment: CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329
    Organism Scientific: BACILLUS AGARADHAERENS
    Organism Taxid: 76935
    Strain: AC13
    Synonym: ENDO-1,4-BETA-GLUCANASE, ALKALINE CELLULASE, CEL5A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1DCB1Ligand/Ion2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:53 , HOH A:2377 , HOH A:2378BINDING SITE FOR RESIDUE SO4 A1307
2AC2SOFTWAREGLU A:22 , ARG A:23 , HIS A:35 , TRP A:39 , TYR A:66 , HIS A:101 , LEU A:103 , ASN A:138 , GLU A:139 , TRP A:178 , TYR A:202 , GLU A:228 , ALA A:234 , THR A:235 , GLY A:236 , TRP A:262 , LYS A:267 , GLU A:269 , HOH A:2037 , HOH A:2368 , HOH A:2369 , HOH A:2370 , HOH A:2371 , HOH A:2372 , HOH A:2373BINDING SITE FOR RESIDUE DCB A1304
3AC3SOFTWAREGLU A:80 , LYS A:83 , GLU A:84 , GLU A:87 , LYS A:152 , GLU A:156 , GLN A:189 , HOH A:2135 , HOH A:2223 , HOH A:2260BINDING SITE FOR RESIDUE GOL A1305
4AC4SOFTWARESER A:13 , ASN A:168 , GLY A:204 , ALA A:233 , HOH A:2013 , HOH A:2015 , HOH A:2038 , HOH A:2374 , HOH A:2375 , HOH A:2376BINDING SITE FOR RESIDUE GOL A1306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H2J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:262 -Ser A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H2J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.GUN5_BACAG158-167  1A:132-141

(-) Exons   (0, 0)

(no "Exon" information available for 1H2J)

(-) 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:300
 aligned with GUN5_BACAG | O85465 from UniProt  Length:0

    Alignment length:300
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
           GUN5_BACAG    30 SVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRAAMYTSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFDEMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQDVHHAADNQLADPNVMYAFHFYAGTHGQNLRDQVDYALDQGAAIFVSEWGTSAATGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGTFVREKIRES 329
               SCOP domains d1h2ja_ A: Endoglucanase Cel5a                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1h2jA00 A:4-303 Glycosidases                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh..eee..eee.........eeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh...eeeeee....................hhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h2j A   4 SVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRAAMYTSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFDEMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQDVHHAADNQLADPNVMYAFHFYAGTHGQNLRDQVDYALDQGAAIFVSEWGTSAATGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGTFVREKIRES 303
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303
   Legend:   → Mismatch (orange background)
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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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H2J)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GUN5_BACAG | O85465)
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: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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  3.2.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        GUN5_BACAG | O85465: 1a3h 1e5j 1h11 1h5v 1hf6 1ocq 1qhz 1qi0 1qi2 1w3k 1w3l 2a3h 2v38 3a3h 4a3h 5a3h 6a3h 7a3h 8a3h

(-) Related Entries Specified in the PDB File

1h11 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION
1h2j ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4- DINITROPHENYL-2-DEOXY-2FLUORO- CELLOBIOSIDE AT 1.15 A RESOLUTION
1h5v THIOPENTASACCHARIDE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHARENS AT 1.1 A RESOLUTION IN THE TETRAGONAL CRYSTAL FORM
1hf5 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION
1hf6 ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH CELLOTRIOSE
5a3h 2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION
6a3h 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.6 ANGSTROM RESOLUTION