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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE ACIDOPHILIC PH ADAPTATION OF A NOVEL ENDO-1,4-BETA-XYLANASE FROM SCYTALIDIUM ACIDOPHILUM
 
Authors :  C. Michaux, J. Wouters
Date :  11 Mar 10  (Deposition) - 28 Jul 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Family 11 Endoxylanase, Acidophilic Adaptation, Structure/Function Relationship, Glycosidase, Hydrolase, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Michaux, J. Pouyez, A. Mayard, P. Vandurm, I. Housen, J. Wouters
Structural Insights Into The Acidophilic Ph Adaptation Of A Novel Endo-1, 4-Beta-Xylanase From Scytalidium Acidophilum
Biochimie V. 92 1407 2010
PubMed-ID: 20621155  |  Reference-DOI: 10.1016/J.BIOCHI.2010.07.003

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A, B, C, D
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Gene: XYL1
    Organism Scientific: SCYTALIDIUM ACIDOPHILUM
    Organism Taxid: 241811

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CXS5Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CXS2Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:35 , TYR A:93 , ARG A:138 , HOH A:459 , HOH A:473BINDING SITE FOR RESIDUE CXS A 206
2AC2SOFTWARESER A:126 , ASP A:127 , ASN A:170 , HOH A:210 , HOH A:227 , HOH A:252 , HOH A:313 , HOH A:572 , THR B:167 , GLY B:169 , ASN B:170 , ASN B:173BINDING SITE FOR RESIDUE CXS A 207
3AC3SOFTWARETYR B:35 , TYR B:93 , ARG B:138 , PRO B:142 , HOH B:309 , HOH B:615 , HOH B:714 , HOH C:496BINDING SITE FOR RESIDUE CXS B 206
4AC4SOFTWARETYR C:35 , TYR C:93 , PRO C:142 , HOH C:546 , HOH C:555BINDING SITE FOR RESIDUE CXS C 206
5AC5SOFTWAREGLN D:33 , TYR D:35 , TYR D:93 , PRO D:142 , HOH D:387 , HOH D:435BINDING SITE FOR RESIDUE CXS D 206

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:115 -A:134
2B:115 -B:134
3C:115 -C:134
4D:115 -D:134

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:98 -Pro A:99
2Ser B:98 -Pro B:99
3Ser C:98 -Pro C:99
4Ser D:98 -Pro D:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M4F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M4F)

(-) Exons   (0, 0)

(no "Exon" information available for 3M4F)

(-) 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:181
 aligned with Q6VAY1_9PEZI | Q6VAY1 from UniProtKB/TrEMBL  Length:205

    Alignment length:181
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
         Q6VAY1_9PEZI    25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeehhhhh..eee....eeeeeee....eeeeeee......eeeeeeeee....eeeeeeeeee....eeeeeeeee.........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeehhhhhhhhhhhh....eeeeeeeeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m4f A  25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with Q6VAY1_9PEZI | Q6VAY1 from UniProtKB/TrEMBL  Length:205

    Alignment length:181
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
         Q6VAY1_9PEZI    25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeehhhhh..eee....eeeeeee....eeeeeee......eeeeeeeee....eeeeeeeeee....eeeeeeeee.........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeehhhhhhhhhhhh....eeeeeeeeeeee.eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m4f B  25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with Q6VAY1_9PEZI | Q6VAY1 from UniProtKB/TrEMBL  Length:205

    Alignment length:181
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
         Q6VAY1_9PEZI    25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeehhhhhh.eee....eeeeeee....eeeeeee......eeeeeeeee....eeeeeeeeee....eeeeeeeee.........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeehhhhhhhhhh......eeeeeeeeeeee.eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m4f C  25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 


Chain D from PDB  Type:PROTEIN  Length:181
 aligned with Q6VAY1_9PEZI | Q6VAY1 from UniProtKB/TrEMBL  Length:205

    Alignment length:181
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
         Q6VAY1_9PEZI    25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeehhhhhh.eee....eeeeeee....eeeeeee......eeeeeeeee....eeeeeeeeee....eeeeeeeee.........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeehhhhhhhhhh......eeeeeeeeeeee.eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m4f D  25 NPGGIDYVQNYNGDVADFQYNEGAGTYTCGWDGSTDFVVGLGWSTGAARDITYSATYNAGGSGSYLAVYGWVNSPQAEYYIVESYGDYNPCSNAEGLGTLESDGSTYTVCTDTRTNEPSITGTSTFTQYWSVRQSERTSGTVTVGNHFNYWAQHGFGDSYNFQVMAVEAFSGSGSASVSVS 205
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
   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 3M4F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M4F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M4F)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6VAY1_9PEZI | Q6VAY1)
molecular function
    GO:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    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: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.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

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  3m4f
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 Related Entries

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