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(-) Description

Title :  XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTETRAOSE
 
Authors :  A. Schmidt, C. Kratky
Date :  15 Dec 98  (Deposition) - 06 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Family 10 Xylanase, Penicillium Simplicissimum, Glycosyl Hydrolase, Substrate Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schmidt, G. M. Gubitz, C. Kratky
Xylan Binding Subsite Mapping In The Xylanase From Penicillium Simplicissimum Using Xylooligosaccharides As Cryo-Protectant.
Biochemistry V. 38 2403 1999
PubMed-ID: 10029534  |  Reference-DOI: 10.1021/BI982108L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (XYLANASE)
    Cellular Location: SECRETED
    Chains: A
    EC Number: 3.2.1.8
    Organism Scientific: PENICILLIUM SIMPLICISSIMUM
    Organism Taxid: 69488
    Other Details: PENICILLIUM SIMPLICISSIMUM (OUDEM.) THOM.

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2XYP3Ligand/IonBETA-D-XYLOPYRANOSE
3XYS1Ligand/IonXYLOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:48 , GLY A:230 , LYS A:261 , XYP A:558BINDING SITE FOR RESIDUE XYP A 557
2AC2SOFTWAREGLU A:47 , ASN A:48 , LYS A:51 , GLN A:91 , TRP A:268 , TRP A:276 , XYP A:557 , XYP A:559BINDING SITE FOR RESIDUE XYP A 558
3AC3SOFTWARELYS A:51 , HIS A:84 , TRP A:88 , ASN A:131 , GLU A:132 , GLN A:208 , GLU A:238 , TRP A:268 , TRP A:276 , HOH A:541 , XYP A:558 , XYS A:560BINDING SITE FOR RESIDUE XYP A 559
4AC4SOFTWAREGLU A:132 , TYR A:175 , GLN A:208 , HIS A:210 , TRP A:276 , HOH A:448 , HOH A:541 , XYP A:559BINDING SITE FOR RESIDUE XYS A 560
5ACTAUTHORGLU A:132 , GLU A:238ACTIVE SITE.

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:256 -A:262

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:84 -Thr A:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B3Y)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_2PS51760 Glycosyl hydrolases family 10 (GH10) domain profile.XYNA_PENSI21-301  1A:21-301
2GH10_1PS00591 Glycosyl hydrolases family 10 (GH10) active site.XYNA_PENSI231-241  1A:231-241

(-) Exons   (0, 0)

(no "Exon" information available for 1B3Y)

(-) 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:302
 aligned with XYNA_PENSI | P56588 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:302
                                    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  
           XYNA_PENSI     1 QASVSIDAKFKAHGKKYLGTIGDQYTLTKNTKNPAIIKADFGQLTPENSMKWDATEPNRGQFTFSGSDYLVNFAQSNGKLIRGHTLVWHSQLPGWVSSITDKNTLISVLKNHITTVMTRYKGKIYAWDVLNEIFNEDGSLRNSVFYNVIGEDYVRIAFETARSVDPNAKLYINDYNLDSAGYSKVNGMVSHVKKWLAAGIPIDGIGSQTHLGAGAGSAVAGALNALASAGTKEIAITELDIAGASSTDYVNVVNACLNQAKCVGITVWGVADPDSWRSSSSPLLFDGNYNPKAAYNAIANAL 302
               SCOP domains d1b3ya_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1b3yA00 A:2-302 Glycosidases                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh....eeeeee.hhhhhh..hhhhhhhhh..eeeee....hhhhh........hhhhhhhhhhhh...eeeeeeeeeeee..hhhh....hhhhhhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhh......eeeeeeee.......hhhhhhh.......eeeeeeeee....hhhhhhhhhhhh....eeeeee....hhh...hhh............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------GH10_2  PDB: A:21-301 UniProt: 21-301                                                                                                                                                                                                                                                    - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b3y A   1 xASVSIDAKFKAHGKKYLGTIGDQYTLTKNTKNPAIIKADFGQLTPENSMKWDATEPNRGQFTFSGSDYLVNFAQSNGKLIRGHTLVWHSQLPGWVSSITDKNTLISVLKNHITTVMTRYKGKIYAWDVLNEIFNEDGSLRNSVFYNVIGEDYVRIAFETARSVDPNAKLYINDYNLDSAGYSKVNGMVSHVKKWLAAGIPIDGIGSQTHLGAGAGSAVAGALNALASAGTKEIAITELDIAGASSTDYVNVVNACLNQAKCVGITVWGVADPDSWRSSSSPLLFDGNYNPKAAYNAIANAL 302
                            |       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  
                            |                                                                                                                                                                                                                                                                                                             
                            1-PCA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B3Y)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_PENSI | P56588)
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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1b3y
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  XYNA_PENSI | P56588
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_PENSI | P56588: 1b30 1b31 1b3v 1b3w 1b3x 1b3z 1bg4

(-) Related Entries Specified in the PDB File

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