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(-) Description

Title :  REASSEMBLY AND CO-CRYSTALLIZATION OF A FAMILY 9 PROCESSIVE ENDOGLUCANASE FROM SEPARATELY EXPRESSED GH9 AND CBM3C MODULES
 
Authors :  S. Petkun, R. Lamed, S. Jindou, T. Burstein, O. Yaniv, Y. Shoham, J. W. L. E. A. Bayer, F. Frolow
Date :  24 May 10  (Deposition) - 22 Jun 11  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Sugar Binding Protein Complex, Family-9 Glycoside Hydrolase, Hydrolase, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Petkun, I. R. Grinberg, R. Lamed, S. Jindou, T. Burstein, O. Yaniv, Y. Shoham, J. W. L. Shimon, E. A. Bayer, F. Frolow
Reassembly And Co-Crystallization Of A Family 9 Processive Endoglucanase From Its Component Parts: Structural And Functional Significance Of Intermodular Linker
Peerj V. 3 E1126 2015
PubMed-ID: 26401442  |  Reference-DOI: 10.7717/PEERJ.1126

(-) Compounds

Molecule 1 - ENDOGLUCANASE 1
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Fragment: GH9 CATALYTIC DOMAIN, RESIDUES 54-516
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: ENDOGLUCANASE I, EGI, ENDO-1,4-BETA-GLUCANASE, CELLULASE I
 
Molecule 2 - ENDOGLUCANASE 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Fragment: CBM3C CELLULOSE BINDING MODULE, RESIDUES 517-683
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: ENDOGLUCANASE I, EGI, ENDO-1,4-BETA-GLUCANASE, CELLULASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:210 , GLY A:211 , ASP A:214 , GLU A:215 , ASP A:261 , HOH A:2470BINDING SITE FOR RESIDUE CA A1447
2AC2SOFTWAREASN B:505 , GLU B:508 , ASN B:578 , ASN B:581 , ASP B:582 , HOH B:2235BINDING SITE FOR RESIDUE CA B1619
3AC3SOFTWARETYR A:81 , ASP A:83 , ALA A:84 , LYS A:441BINDING SITE FOR RESIDUE CL A1448
4AC4SOFTWAREGLN A:11 , GLN A:90 , HIS A:93BINDING SITE FOR RESIDUE CL A1449
5AC5SOFTWAREASN A:207 , SER A:208 , LYS B:538BINDING SITE FOR RESIDUE CL A1450

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:1 -Gly A:2
2Glu A:390 -Pro A:391
3Trp B:490 -Pro B:491
4Glu B:615 -His B:616

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 4)

Asymmetric/Biological Unit (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F9_1PS00592 Glycosyl hydrolases family 9 active sites signature 1.GUNI_CLOTH434-450  1A:362-378
2GLYCOSYL_HYDROL_F9_2PS00698 Glycosyl hydrolases family 9 active sites signature 2.GUNI_CLOTH484-502  1A:412-430
3CBM3PS51172 CBM3 (carbohydrate binding type-3) domain profile.GUNI_CLOTH529-684
 
736-887		  2A:445-445
B:459-613
-

(-) Exons   (0, 0)

(no "Exon" information available for 2XFG)

(-) 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:446
 aligned with GUNI_CLOTH | Q02934 from UniProtKB/Swiss-Prot  Length:887

    Alignment length:462
                                    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       402       412       422       432       442       452       462       472       482       492       502       512       522       532  
           GUNI_CLOTH    73 TGAFNYGEALQKAIFFYECQRSGKLDPSTLRLNWRGDSGLDDGKDAGIDLTGGWYDAGDHVKFNLPMSYSAAMLGWAVYEYEDAFKQSGQYNHILNNIKWACDYFIKCHPEKDVYYYQVGDGHADHAWWGPAEVMPMERPSYKVDRSSPGSTVVAETSAALAIASIIFKKVDGEYSKECLKHAKELFEFADTTKSDDGYTAANGFYNSWSGFYDELSWAAVWLYLATNDSSYLDKAESYSDKWGYEPQTNIPKYKWAQCWDDVTYGTYLLLARIKNDNGKYKEAIERHLDWWTTGYNGERITYTPKGLAWLDQWGSLRYATTTAFLACVYSDWENGDKEKAKTYLEFARSQADYALGSTGRSFVVGFGENPPKRPHHRTAHGSWADSQMEPPEHRHVLYGALVGGPDSTDNYTDDISNYTCNEVACDYNAGFVGLLAKMYKLYGGSPDPKFNGIEEVPEDEI 534
               SCOP domains d2xfga_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----Glyco_hydro_9-2xfgA01 A:5-437                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh......................hhhhh..............eehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhh...hhhhh.....eeeee....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...................hhhhhh...................................hhhhhh.hhhhhhhhhhhhhhhhhhhh----------------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F---------------------------------GLYCOSYL_HYDROL_F9_--------------------------CBM3   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xfg A   1 TGAFNYGEALQKAIFFYECQRSGKLDSSTLRLNWRGDSGLDDGKDAGIDLTGGWYDAGDHVKFNLPMSYSAAMLGWAVYEYEDAFKQSGQYNHILNNIKWACDYFIKCHPEKDVYYYQVGDGHADHAWWGPAEVMPMERPSYKVDRSSPGSTVVAETSAALAIASIIFKKVDGEYSKECLKHAKELFEFADTTKSDDGYTAANGFYNSWSGFYDELSWAAVWLYLATNDSSYLDKAESYSDKWGYEPQTNIPKYKWAQCWDDVTYGTYLLLARIKNDNGKYKEAIERHLDWWTTGYNGERITYTPKGLAWLDQWGSLRYATTTAFLACVYSDWENGDKEKAKTYLEFARSQADYALGSTGRSFVVGFGENPPKRPHHRTAHGSWADSQMEPPEHRHVLYGALVGGPDSTDNYTDDISNYTCNEVACDYNAGFVGLLAKMYKLYG----------------EL 446
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       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   |     -         -| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     444              445 


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with GUNI_CLOTH | Q02934 from UniProtKB/Swiss-Prot  Length:887

    Alignment length:199
                                   526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706         
           GUNI_CLOTH   517 GSPDPKFNGIEEVPEDEIFVEAGVNASGNNFIEIKAIVNNKSGWPARVCENLSFRYFINIEEIVNAGKSASDLQVSSSYNQGAKLSDVKHYKDNIYYVEVDLSGTKIYPGGQSAYKKEVQFRISAPEGTVFNPENDYSYQGLSAGTVVKSEYIPVYDAGVLVFGREPGSASKSTSKDNGLSKATPTVKTESQPTAKHTQ 715
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------CBM_3-2xfgB01 B:464-547                                                             -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeeee..eeeeeeeeee...........eeeeeeeehhhhhh...hhhhheee.......ee...eeee..eeeeeee..............eeeeeeeee.......hhhhhhhhh.......ee.....eee..eeee....---------------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------CBM3  PDB: B:459-613 UniProt: 529-684                                                                                                                       ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xfg B 447 GSPDPKFNGIEEVPEDEIFVEAGVNASGNNFIEIKAIVNNKSGWPARVCENLSFRYFINIEEIVNAGKSASDLQVSSSYNQGAKLSDVKHYKDNIYYVEVDLSGTKIYPGGQSAYKKEVQFRISAPEGTVFNPENDYSYQGLSAGTVVKSEYIPVYDAGVLVFGREP---------------------------LEHHH 618
                                   456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606      |  -         -         -    |    
                                                                                                                                                                                                613                         614
   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  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: 6_Hairpin (120)
(-)
Clan: CBD (21)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GUNI_CLOTH | Q02934)
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: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:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
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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