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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA FUSCA ENDOGLUCANASE CEL5A (E5)
 
Authors :  G. I. Berglund, P. J. Gualfetti, C. Requadt, L. S. Gross, T. Bergfors, A. Shaw, M. Saldajeno, C. Mitchinson, M. Sandgren
Date :  21 Apr 06  (Deposition) - 29 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbohydrate Metabolism, Polysaccharide Degradation, Glycoside Hydrolase Family 5, Hydrolase, Glycosidase, Endoglucanase, Thermobifida Fusca E5, Cellulose Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. I. Berglund, P. J. Gualfetti, C. Requadt, L. S. Gross, T. Bergfors, A. Shaw, M. Saldajeno, C. Mitchinson, M. Sandgren
The Crystal Structure Of The Catalytic Domain Of Thermobifida Fusca Endoglucanase Cel5A In Complex With Cellotetraose
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENDOGLUCANASE E-5
    Chains: A, B
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PBS42
    Expression System Taxid: 1423
    Fragment: CATALYTIC DOMAIN, RESIDUES 161-466
    Organism Scientific: THERMOBIFIDA FUSCA
    Organism Taxid: 2021
    Synonym: ENDOGLUCANASE CEL5A, ENDO-1,4-BETA-GLUCANASE E-4, CELLULASE E-5, CELLULASE E5

 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  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1BEN2Ligand/IonBENZAMIDINE
2NA4Ligand/IonSODIUM ION
3ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:169 , ASP A:173 , HIS B:233 , LEU B:236 , GLU B:278BINDING SITE FOR RESIDUE ZN A1432
02AC2SOFTWAREALA A:251 , ASP A:287 , ASP A:289 , NA A:1436 , HOH A:2188 , HOH A:2192 , HOH A:2322BINDING SITE FOR RESIDUE ZN A1433
03AC3SOFTWAREASP A:193 , HOH A:2323 , HOH A:2324BINDING SITE FOR RESIDUE ZN A1434
04AC4SOFTWAREGLU A:263 , GLU A:355 , NA A:1437 , HOH A:2325 , HOH A:2326BINDING SITE FOR RESIDUE ZN A1435
05AC5SOFTWAREALA A:251 , LYS A:253 , ASP A:287 , ASP A:289 , SER A:290 , ZN A:1433 , HOH A:2184 , HOH A:2190 , HOH A:2192 , HOH A:2322BINDING SITE FOR RESIDUE NA A1436
06AC6SOFTWAREZN A:1435 , HOH A:2226 , HOH A:2326BINDING SITE FOR RESIDUE NA A1437
07AC7SOFTWAREHIS A:233 , LEU A:236 , GLU A:278 , ASP B:169 , ASP B:173BINDING SITE FOR RESIDUE ZN B1432
08AC8SOFTWAREGLU B:145 , HIS B:146BINDING SITE FOR RESIDUE ZN B1433
09AC9SOFTWAREALA B:251 , LYS B:253 , ASP B:287 , ASP B:289 , NA B:1437 , HOH B:2312 , HOH B:2313BINDING SITE FOR RESIDUE ZN B1434
10BC1SOFTWAREGLU B:263 , GLU B:355 , HOH B:2103 , HOH B:2314BINDING SITE FOR RESIDUE ZN B1435
11BC2SOFTWAREASP B:193BINDING SITE FOR RESIDUE NA B1436
12BC3SOFTWAREALA B:251 , LYS B:253 , ASP B:287 , ASP B:289 , ZN B:1434 , HOH B:2187 , HOH B:2312 , HOH B:2313BINDING SITE FOR RESIDUE NA B1437
13BC4SOFTWAREARG A:284 , SER A:321 , HOH A:2186 , HOH A:2220 , HOH A:2319 , HOH A:2320 , HOH A:2321BINDING SITE FOR RESIDUE BEN A1431
14BC5SOFTWAREARG B:284 , ALA B:320 , SER B:321 , HOH B:2215 , HOH B:2309 , HOH B:2310 , HOH B:2311BINDING SITE FOR RESIDUE BEN B1431

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:138 -A:143
2A:166 -A:406
3B:138 -B:143
4B:166 -B:406

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:228 -Pro A:229
2Trp A:389 -Asn A:390
3Gly A:410 -Pro A:411
4Thr B:228 -Pro B:229
5Trp B:389 -Asn B:390
6Gly B:410 -Pro B:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.GUN5_THEFU292-301
 		  2A:256-265
B:256-265
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.GUN5_THEFU292-301
 		  1A:256-265
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.GUN5_THEFU292-301
 		  1-
B:256-265

(-) Exons   (0, 0)

(no "Exon" information available for 2CKS)

(-) 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:305
 aligned with GUN5_THEFU | Q01786 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:305
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461     
           GUN5_THEFU   162 GTPVERYGKVQVCGTQLCDEHGNPVQLRGMSTHGIQWFDHCLTDSSLDALAYDWKADIIRLSMYIQEDGYETNPRGFTDRMHQLIDMATARGLYVIVDWHILTPGDPHYNLDRAKTFFAEIAQRHASKTNVLYEIANEPNGVSWASIKSYAEEVIPVIRQRDPDSVIIVGTRGWSSLGVSEGSGPAEIAANPVNASNIMYAFHFYAASHRDNYLNALREASELFPVFVTEFGTETYTGDGANDFQMADRYIDLMAERKIGWTKWNYSDDFRSGAVFQPGTCASGGPWSGSSLKASGQWVRSKLQS 466
               SCOP domains d2cksa_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2cksA00 A:126-430 Glycosidases                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eee..eee.........eeee..hhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhh....eee.hhhhhh.hhhhh..hhhhhhh......eeeeeeee....hhhhhhhhhhhhhhh.eeeeeee..........hhhhhhhhhhhhhhhh..eeee..............hhhhhh...hhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cks A 126 GTPVERYGKVQVCGTQLCDEHGNPVQLRGMSTHGIQWFDHCLTDSSLDALAYDWKADIIRLSMYIQEDGYETNPRGFTDRMHQLIDMATARGLYVIVDWHILTPGDPHYNLDRAKTFFAEIAQRHASKTNVLYEIANEPNGVSWASIKSYAEEVIPVIRQRDPDSVIIVGTRGWSSLGVSEGSGPAEIAANPVNASNIMYAFHFYAASHRDNYLNALREASELFPVFVTEFGTETYTGDGANDFQMADRYIDLMAERKIGWTKWNYSDDFRSGAVFQPGTCASGGPWSGSSLKASGQWVRSKLQS 430
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425     


Chain B from PDB  Type:PROTEIN  Length:306
 aligned with GUN5_THEFU | Q01786 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:306
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460      
           GUN5_THEFU   161 TGTPVERYGKVQVCGTQLCDEHGNPVQLRGMSTHGIQWFDHCLTDSSLDALAYDWKADIIRLSMYIQEDGYETNPRGFTDRMHQLIDMATARGLYVIVDWHILTPGDPHYNLDRAKTFFAEIAQRHASKTNVLYEIANEPNGVSWASIKSYAEEVIPVIRQRDPDSVIIVGTRGWSSLGVSEGSGPAEIAANPVNASNIMYAFHFYAASHRDNYLNALREASELFPVFVTEFGTETYTGDGANDFQMADRYIDLMAERKIGWTKWNYSDDFRSGAVFQPGTCASGGPWSGSSLKASGQWVRSKLQS 466
               SCOP domains d2cksb_ B: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2cksB00 B:125-430 Glycosidases                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh..eee..eee.........eeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhhhhhh...eeee.hhhhhh.hhhhh..hhhhhhh......eeeeeeee....hhhhhhhhhhhhhhh.eeeeeee..........hhhhhhhhhhhhhhhh.eeeeeee.....................hhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cks B 125 TGTPVERYGKVQVCGTQLCDEHGNPVQLRGMSTHGIQWFDHCLTDSSLDALAYDWKADIIRLSMYIQEDGYETNPRGFTDRMHQLIDMATARGLYVIVDWHILTPGDPHYNLDRAKTFFAEIAQRHASKTNVLYEIANEPNGVSWASIKSYAEEVIPVIRQRDPDSVIIVGTRGWSSLGVSEGSGPAEIAANPVNASNIMYAFHFYAASHRDNYLNALREASELFPVFVTEFGTETYTGDGANDFQMADRYIDLMAERKIGWTKWNYSDDFRSGAVFQPGTCASGGPWSGSSLKASGQWVRSKLQS 430
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GUN5_THEFU | Q01786)
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.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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
        GUN5_THEFU | Q01786: 2ckr

(-) Related Entries Specified in the PDB File

2ckr X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA FUSCA ENDOGLUCANASE CEL5A (E5) E355Q IN COMPLEX WITH CELLOTETRAOSE