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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-D-XYLOSIDASE FROM THERMOANAEROBACTERIUM SACCHAROLYTICUM, A FAMILY 39 GLYCOSIDE HYDROLASE
 
Authors :  J. K. Yang, H. J. Yoon, H. J. Ahn, B. Il Lee, J. D. Pedelacq, E. C. Liong, J. Berendzen, M. Laivenieks, C. Vieille, G. J. Zeikus, D. J. Vocadlo, S. G. Withers, S. W. Suh
Date :  03 Jul 03  (Deposition) - 23 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Family 39 Glycoside Hydrolase, Xylosidase, Xylan, Xylose, Covalent Glycosyl-Enzyme Intermediate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Yang, H. J. Yoon, H. J. Ahn, B. I. Lee, J. D. Pedelacq, E. C. Liong, J. Berendzen, M. Laivenieks, C. Vieille, G. J. Zeikus, D. J. Vocadlo, S. G. Withers, S. W. Suh
Crystal Structure Of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycosid Hydrolase.
J. Mol. Biol. V. 335 155 2004
PubMed-ID: 14659747  |  Reference-DOI: 10.1016/J.JMB.2003.10.026

(-) Compounds

Molecule 1 - BETA-XYLOSIDASE
    Chains: A, B
    EC Number: 3.2.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXHP3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOANAEROBACTERIUM SACCHAROLYTICUM
    Organism Taxid: 28896
    Synonym: 1,4-BETA-D-XYLOSIDASE, 1,4-BETA-D-XYLAN XYLOHYDROLASE, XYLAN 1,4-BETA-XYLOSIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1XYP2Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1XYP4Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:54 , PHE A:115 , ASN A:159 , GLU A:160 , GLU A:277 , TYR A:282 , TRP A:315 , PHE A:321 , GLU A:323 , PHE A:335 , HOH A:1290BINDING SITE FOR RESIDUE XYP A 601
2AC2SOFTWAREHIS B:54 , PHE B:115 , ASN B:159 , GLU B:160 , GLU B:277 , TYR B:282 , TRP B:315 , PHE B:321 , GLU B:323 , PHE B:335BINDING SITE FOR RESIDUE XYP B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PX8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:101 -Phe A:102
2Gly A:197 -Pro A:198
3Trp A:315 -Thr A:316
4Gly B:101 -Phe B:102
5Gly B:197 -Pro B:198
6Trp B:315 -Thr B:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PX8)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F39PS01027 Glycosyl hydrolases family 39 active site.XYNB_THESA153-162
 		  2A:153-162
B:153-162
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F39PS01027 Glycosyl hydrolases family 39 active site.XYNB_THESA153-162
 		  4A:153-162
B:153-162

(-) Exons   (0, 0)

(no "Exon" information available for 1PX8)

(-) 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:500
 aligned with XYNB_THESA | P36906 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:500
                                    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       450       460       470       480       490       500
           XYNB_THESA     1 MIKVRVPDFSDKKFSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLEIGIRPFVEIGFMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGGADYWIEDFLNFCYEENVPVDFVSRHATTSKQGEYTPHLIYQEIMPSEYMLNEFKTVREIIKNSHFPNLPFHITEYNTSYSPQNPVHDTPFNAAYIARILSEGGDYVDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFNAMGEEMLYRDEHMLVTRRDDGSVALIAWNEVMDKTENPDEDYEVEIPVRFRDVFIKRQLIDEEHGNPWGTWIHMGRPRYPSKEQVNTLREVAKPEIMTSQPVANDGYLNLKFKLGKNAVVLYELTERIDESSTYIGLDDSKINGY 500
               SCOP domains d1px8a1      d1px8a2 A:14-359 Beta-D-xylosidase, catalytic domain                                                                                                                                                                                                                                                                                                      d1px8a1 A:1-13,A:360-500 Beta-D-xylosidase                                                                                                    SCOP domains
               CATH domains 1px8A01       1px8A02 A:15-358 Glycosidases                                                                                                                                                                                                                                                                                                                           1px8A01 A:1-14,A:359-500 Glycosyl hydrolase domain; family 39                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.........hhhhh.eee..hhhhhhhhhhhhhhhhhhhhh...eee...........eeeeee..eeeeee.hhhhhhhhhhhhhh..ee..ee...hhhhh....ee....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.......................ee...eehhhhhhhhhhhhh..eeeeee..eeeee.....eeeeeee..........eeeeeeee.....eeeeeeee.....hhhhhhhhh......hhhhhhhhhhhh..eeeee.......eeeeeeee...eeeeeeeee...hhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1px8 A   1 MIKVRVPDFSDKKFSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLEIGIRPFVEIGFMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGGADYWIEDFLNFCYEENVPVDFVSRHAYTSKQGEYTPHLIYQEIMPSEYMLNEFKTVREIIKNSHFPNLPFHITEYNTSYSPQNPVHDTPFNAAYIARILSEGGDYVDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFNAMGEEMLYRDEHMLVTRRDDGSVALIAWNEVMDKTENPDEDYEVEIPVRFRDVFIKRQLIDEEHGNPWGTWIHMGRPRYPSKEQVNTLREVAKPEIMTSQPVANDGYLNLKFKLGKNAVVLYELTERIDESSTYIGLDDSKINGY 500
                                    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       450       460       470       480       490       500


Chain B from PDB  Type:PROTEIN  Length:500
 aligned with XYNB_THESA | P36906 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:500
                                    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       450       460       470       480       490       500
           XYNB_THESA     1 MIKVRVPDFSDKKFSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLEIGIRPFVEIGFMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGGADYWIEDFLNFCYEENVPVDFVSRHATTSKQGEYTPHLIYQEIMPSEYMLNEFKTVREIIKNSHFPNLPFHITEYNTSYSPQNPVHDTPFNAAYIARILSEGGDYVDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFNAMGEEMLYRDEHMLVTRRDDGSVALIAWNEVMDKTENPDEDYEVEIPVRFRDVFIKRQLIDEEHGNPWGTWIHMGRPRYPSKEQVNTLREVAKPEIMTSQPVANDGYLNLKFKLGKNAVVLYELTERIDESSTYIGLDDSKINGY 500
               SCOP domains d1px8b1      d1px8b2 B:14-359 Beta-D-xylosidase, catalytic domain                                                                                                                                                                                                                                                                                                      d1px8b1 B:1-13,B:360-500 Beta-D-xylosidase                                                                                                    SCOP domains
               CATH domains 1px8B01       1px8B02 B:15-358 Glycosidases                                                                                                                                                                                                                                                                                                                           1px8B01 B:1-14,B:359-500 Glycosyl hydrolase domain; family 39                                                                                  CATH domains
           Pfam domains (1) Glyco_hydro_39-1px8B01 B:1-482                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (1)
           Pfam domains (2) Glyco_hydro_39-1px8B02 B:1-482                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (2)
         Sec.struct. author ..eee.........hhhhh.eee..hhhhhhhhhhhhhhhhhhhhh...eee...........eeeeee..eeeeee.hhhhhhhhhhhhhh..ee..ee...hhhhh....ee....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.......................ee...eehhhhhhhhhhhhh..eeeeee..eeeee.....eeeeeee..........eeeeeeee.....eeeeeeee.....hhhhhhhhh......hhhhhhhhhhhh..eeeee.......eeeeeeee...eeeeeeeee...hhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1px8 B   1 MIKVRVPDFSDKKFSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLEIGIRPFVEIGFMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGGADYWIEDFLNFCYEENVPVDFVSRHAYTSKQGEYTPHLIYQEIMPSEYMLNEFKTVREIIKNSHFPNLPFHITEYNTSYSPQNPVHDTPFNAAYIARILSEGGDYVDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFNAMGEEMLYRDEHMLVTRRDDGSVALIAWNEVMDKTENPDEDYEVEIPVRFRDVFIKRQLIDEEHGNPWGTWIHMGRPRYPSKEQVNTLREVAKPEIMTSQPVANDGYLNLKFKLGKNAVVLYELTERIDESSTYIGLDDSKINGY 500
                                    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       450       460       470       480       490       500
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XYNB_THESA | P36906)
molecular function
    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:0009044    xylan 1,4-beta-xylosidase activity    Catalysis of the hydrolysis of (1->4)-beta-D-xylans so as to remove successive D-xylose residues from the non-reducing termini.
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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  1px8
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNB_THESA | P36906: 1uhv

(-) Related Entries Specified in the PDB File

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