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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INACTIVE KEMP ELIMINATION DESIGN HG-1
 
Authors :  L. M. Thomas, H. K. Privett, S. L. Mayo
Date :  22 Jul 10  (Deposition) - 20 Jul 11  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Kemp Eliminase, Kemp Elimination, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. K. Privett, G. Kiss, T. M. Lee, R. Blomberg, R. A. Chica, L. M. Thomas, D. Hilvert, K. N. Houk, S. L. Mayo
Iterative Approach To Computational Enzyme Design.
Proc. Natl. Acad. Sci. Usa V. 109 3790 2012
PubMed-ID: 22357762  |  Reference-DOI: 10.1073/PNAS.1118082108

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-329
    Gene: XYNA
    Mutation: YES
    Organism Scientific: THERMOASCUS AURANTIACUS
    Organism Taxid: 5087
    Synonym: XYLANASE, 1,4-BETA-D-XYLAN XYLANOHYDROLASE, TAXI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3O2L)

(-) Sites  (0, 0)

(no "Site" information available for 3O2L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O2L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:83 -Thr A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O2L)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_2PS51760 Glycosyl hydrolases family 10 (GH10) domain profile.XYNA_THEAU29-326  1A:3-300
2GH10_1PS00591 Glycosyl hydrolases family 10 (GH10) active site.XYNA_THEAU256-266  1A:230-240

(-) Exons   (0, 0)

(no "Exon" information available for 3O2L)

(-) 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:306
 aligned with XYNA_THEAU | P23360 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:306
                                                                                                                                                                                                                                                                                                                                         329  
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325   |  
           XYNA_THEAU    26 RQAAQSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGQVTPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIRGHTLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVNEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYINDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVAITELDVAGASPTDYVNVVNACLNVQSCVGITVWGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQ--   -
               SCOP domains d3o2la_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...eeeeeehhhhhh..hhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhh..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.....eeee..ee...hhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---GH10_2  PDB: A:3-300 UniProt: 29-326                                                                                                                                                                                                                                                                      ----- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ----------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o2l A   0 AEAAQSVDQLIKARGKVYFGVMTDQNRLTTGKNAAIIQADFGQVTPMNSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIRGHTLVGHFYLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVNEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYINDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVAITELNVAGASPTDYVNVVNACLNVQSCVGITVAGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQGS 305
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O2L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O2L)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_THEAU | P23360)
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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  Cis Peptide Bonds
    His A:83 - Thr A:84   [ RasMol ]  
 

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  3o2l
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  XYNA_THEAU | P23360
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  3.2.1.8
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_THEAU | P23360: 1gok 1gom 1goo 1goq 1gor 1i1w 1i1x 1k6a 1tux 2bnj 3nyd 4bs0

(-) Related Entries Specified in the PDB File

3nyd HG-2