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(-) Description

Title :  THERMOBIFIDA FUSCA CELLOBIOHYDROLASE CEL6B CATALYTIC MUTANT D274A COCRYSTALLIZED WITH CELLOBIOSE
 
Authors :  M. Wu, T. V. Vuong, D. B. Wilson, M. Sandgren, J. Stahlberg, H. Hansson
Date :  28 May 12  (Deposition) - 12 Jun 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Cellulose Degradation, Glycoside Hydrolase Family 6, Cellulase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wu, L. Bu, T. V. Vuong, D. B. Wilson, M. F. Crowley, M. Sandgren, J. Stahlberg, G. T. Beckham, H. Hansson
Loop Motions Important To Product Expulsion In The Thermobifida Fusca Glycoside Hydrolase Family 6 Cellobiohydrolase From Structural And Computational Studies.
J. Biol. Chem. V. 288 33107 2013
PubMed-ID: 24085303  |  Reference-DOI: 10.1074/JBC.M113.502765

(-) Compounds

Molecule 1 - BETA-1,4-EXOCELLULASE
    Chains: A
    EC Number: 3.2.1.91
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RPIL
    Fragment: CATALYTIC DOMAIN, RESIDUES 177-596
    Mutation: YES
    Organism Scientific: THERMOBIFIDA FUSCA
    Organism Taxid: 269800
    Strain: YX
    Synonym: 1,4-BETA-CELLOBIOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BGC6Ligand/IonBETA-D-GLUCOSE
3CA1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:142 , ASP A:419 , HOH A:2006 , HOH A:2007 , HOH A:2008 , HOH A:2191BINDING SITE FOR RESIDUE CA A 607
2AC2SOFTWAREASP A:211 , ASP A:341 , HOH A:2178BINDING SITE FOR RESIDUE ACT A 608
3AC3SOFTWARETRP A:177 , ASP A:179 , TYR A:220 , ASP A:226 , ALA A:229 , SER A:232 , ILE A:273 , THR A:281 , ASN A:282 , HIS A:326 , GLY A:328 , TRP A:329 , TRP A:332 , SER A:334 , ASN A:335 , ALA A:365 , ASN A:366 , ASP A:393 , HIS A:460 , PRO A:461 , GLY A:462 , TRP A:464 , LYS A:491 , PRO A:492 , GLU A:495 , ASP A:497 , LYS A:509 , ARG A:524 , SER A:539 , GLY A:540 , HOH A:2066 , HOH A:2084 , HOH A:2090 , HOH A:2091 , HOH A:2092 , HOH A:2095 , HOH A:2136 , HOH A:2169 , HOH A:2194 , HOH A:2196 , HOH A:2214 , HOH A:2263 , HOH A:2303 , HOH A:2304BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 601 TO 606

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:227 -A:292
2A:465 -A:515

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:555 -Pro A:556

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AVO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AVO)

(-) Exons   (0, 0)

(no "Exon" information available for 4AVO)

(-) 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:420
 aligned with Q47SA9_THEFY | Q47SA9 from UniProtKB/TrEMBL  Length:596

    Alignment length:420
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596
         Q47SA9_THEFY   177 EKVDNPFEGAKLYVNPVWSAKAAAEPGGSAVANESTAVWLDRIGAIEGNDSPTTGSMGLRDHLEEAVRQSGGDPLTIQVVIYNLPGRDCAALASNGELGPDELDRYKSEYIDPIADIMWDFADYENLRIVAIIEIDSLPNLVTNVGGNGGTELCAYMKQNGGYVNGVGYALRKLGEIPNVYNYIDAAHHGWIGWDSNFGPSVDIFYEAANASGSTVDYVHGFISNTANYSATVEPYLDVNGTVNGQLIRQSKWVDWNQYVDELSFVQDLRQALIAKGFRSDIGMLIDTSRNGWGGPNRPTGPSSSTDLNTYVDESRIDRRIHPGNWCNQAGAGLGERPTVNPAPGVDAYVWVKPPGESDGASEEIPNDEGKGFDRMCDPTYQGNARNGNNPSGALPNAPISGHWFSAQFRELLANAYPPL 596
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhh..hhhhh......eee..hhhhhh.........hhhhhhhhhhhhhh...eeeeeee....................hhhhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhh....hhhhh.eeee.................ee..ee.hhh.........hhhhhhhhhhhhhhhhh.....eeeee...................hhhhhhhhhh......................eeeee..eeeee.......................hhhhh.....hhhhh................hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4avo A 139 EKVDNPFEGAKLYVNPVWSAKAAAEPGGSAVANESTAVWLDRIGAIEGNDSPTTGSMGLRDHLEEAVRQSGGDPLTIQVVIYNLPGRDCAALASNGELGPDELDRYKSEYIDPIADIMWDFADYENLRIVAIIEIASLPNLVTNVGGNGGTELCAYMKQNGGYVNGVGYALRKLGEIPNVYNYIDAAHHGWIGWDSNFGPSVDIFYEAANASGSTVDYVHGFISNTANYSATVEPYLDVNGTVNGQLIRQSKWVDWNQYVDELSFVQDLRQALIAKGFRSDIGMLIDTSRNGWGGPNRPTGPSSSTDLNTYVDESRIDRRIHPGNWCNQAGAGLGERPTVNPAPGVDAYVWVKPPGESDGASEEIPNDEGKGFDRMCDPTYQGNARNGNNPSGALPNAPISGHWFSAQFRELLANAYPPL 558
                                   148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558


Chain A from PDB  Type:PROTEIN  Length:420
 aligned with Q60029_THEFU | Q60029 from UniProtKB/TrEMBL  Length:596

    Alignment length:420
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596
         Q60029_THEFU   177 EKVDNPFEGAKLYVNPVWSAKAAAEPGGSAVANESTAVWLDRIGAIEGNDSPTTGSMGLRDHLEEAVRQSGGDPLTIQVVIYNLPGRDCAALASNGELGPDELDRYKSEYIDPIADIMWDFADYENLRIVAIIEIDSLPNLVTNVGGNGGTELCAYMKQNGGYVNGVGYALRKLGEIPNVYNYIDAAHHGWIGWDSNFGPSVDIFYEAANASGSTVDYVHGFISNTANYSATVEPYLDVNGTVNGQLIRQSKWVDWNQYVDELSFVQDLRQALIAKGFRSDIGMLIDTSRNGWGGPNRPTGPSSSTDLNTYVDESRIDRRIHPGNWCNQAGAGLGERPTVNPAPGVDAYVWVKPPGESDGASEEIPNDEGKGFDRMCDPTYQGNARNGNNPSGALPNAPISGHWFSAQFRELLANAYPPL 596
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhh..hhhhh......eee..hhhhhh.........hhhhhhhhhhhhhh...eeeeeee....................hhhhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhh....hhhhh.eeee.................ee..ee.hhh.........hhhhhhhhhhhhhhhhh.....eeeee...................hhhhhhhhhh......................eeeee..eeeee.......................hhhhh.....hhhhh................hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4avo A 139 EKVDNPFEGAKLYVNPVWSAKAAAEPGGSAVANESTAVWLDRIGAIEGNDSPTTGSMGLRDHLEEAVRQSGGDPLTIQVVIYNLPGRDCAALASNGELGPDELDRYKSEYIDPIADIMWDFADYENLRIVAIIEIASLPNLVTNVGGNGGTELCAYMKQNGGYVNGVGYALRKLGEIPNVYNYIDAAHHGWIGWDSNFGPSVDIFYEAANASGSTVDYVHGFISNTANYSATVEPYLDVNGTVNGQLIRQSKWVDWNQYVDELSFVQDLRQALIAKGFRSDIGMLIDTSRNGWGGPNRPTGPSSSTDLNTYVDESRIDRRIHPGNWCNQAGAGLGERPTVNPAPGVDAYVWVKPPGESDGASEEIPNDEGKGFDRMCDPTYQGNARNGNNPSGALPNAPISGHWFSAQFRELLANAYPPL 558
                                   148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558
   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 4AVO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AVO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AVO)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q47SA9_THEFY | Q47SA9)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

Chain A   (Q60029_THEFU | Q60029)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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 Databases and Analysis Tools

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  4avo
    Family and Domain Information: ProDom | SYSTERS
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  Q47SA9_THEFY | Q47SA9
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  Q60029_THEFU | Q60029
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  3.2.1.91
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 Related Entries

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

UniProtKB/TrEMBL
        Q47SA9_THEFY | Q47SA9: 4avn
        Q60029_THEFU | Q60029: 4b4f 4b4h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4AVO)