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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLANASE 10B FROM THERMOTOGA PETROPHILA RKU-1 IN COMPLEX WITH XYLOBIOSE
 
Authors :  C. R. Santos, A. N. Meza, D. M. Trindade, R. Ruller, F. M. Squina, R. A. Pra M. T. Murakami
Date :  16 Jun 10  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim Barrel, Xylanase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Santos, A. N. Meza, Z. B. Hoffmam, J. C. Silva, T. M. Alvarez, R. Ruller, G. M. Giesel, H. Verli, F. M. Squina, R. A. Prade, M. T. Murakami
Thermal-Induced Conformational Changes In The Product Release Area Drive The Enzymatic Activity Of Xylanases 10B: Crystal Structure, Conformational Stability And Functional Characterization Of The Xylanase 10B From Thermotoga Petrophila Rku-1.
Biochem. Biophys. Res. Commun. V. 403 214 2010
PubMed-ID: 21070746  |  Reference-DOI: 10.1016/J.BBRC.2010.11.010

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21 TO 344
    Gene: TPET_0854
    Organism Scientific: THERMOTOGA PETROPHILA RKU-1
    Organism Taxid: 390874
    Strain: RKU-1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SO44Ligand/IonSULFATE ION
3XYP4Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO42Ligand/IonSULFATE ION
3XYP2Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO42Ligand/IonSULFATE ION
3XYP2Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:199 , ALA A:200 , TYR B:235BINDING SITE FOR RESIDUE ACT A 342
02AC2SOFTWARESER A:45 , LYS A:302 , LYS B:215BINDING SITE FOR RESIDUE SO4 A 343
03AC3SOFTWAREPRO A:74 , ASN A:80 , HOH A:405 , HOH A:431 , ARG B:78BINDING SITE FOR RESIDUE SO4 A 344
04AC4SOFTWAREGLU A:64 , ASN A:65 , LYS A:68 , GLN A:108 , TRP A:297 , TRP A:305 , XYP A:346BINDING SITE FOR RESIDUE XYP A 345
05AC5SOFTWARELYS A:68 , HIS A:101 , TRP A:105 , ASN A:149 , GLU A:150 , GLN A:225 , GLU A:256 , TRP A:297 , TRP A:305 , XYP A:345BINDING SITE FOR RESIDUE XYP A 346
06AC6SOFTWARETYR B:193 , GLN B:225 , HIS B:227 , XYP B:346 , HOH B:372BINDING SITE FOR RESIDUE ACT B 342
07AC7SOFTWAREMET B:17 , LYS B:28BINDING SITE FOR RESIDUE SO4 B 343
08AC8SOFTWARELYS A:247 , PRO B:110 , GLY B:111 , HOH B:379BINDING SITE FOR RESIDUE SO4 B 344
09AC9SOFTWAREGLU B:64 , ASN B:65 , LYS B:68 , GLN B:108 , TRP B:297 , TRP B:305 , XYP B:346BINDING SITE FOR RESIDUE XYP B 345
10BC1SOFTWARELYS B:68 , HIS B:101 , TRP B:105 , ASN B:149 , GLU B:150 , GLN B:225 , GLU B:256 , TRP B:297 , TRP B:305 , ACT B:342 , XYP B:345 , HOH B:462BINDING SITE FOR RESIDUE XYP B 346

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NJ3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:101 -Thr A:102
2His B:101 -Thr B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NJ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NJ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3NJ3)

(-) 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:327
 aligned with A5IL00_THEP1 | A5IL00 from UniProtKB/TrEMBL  Length:347

    Alignment length:332
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342  
         A5IL00_THEP1    13 GCVPVFSSQNVSLRELAEKLNIYIGFAAINNFWSLSDEEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENNMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWTKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEDYYLKKQAEICAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIE 344
               SCOP domains d     3nj3a_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----.....hhhhhhhhh..eeeeee..hhhhh.hhhhhhhhhhhhh.eeee....hhhhhh....eeehhhhhhhhhhhhhh..eeeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee..eee....hhhhhhhhhhhhhhh..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhh..ee...........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nj3 A  15 G-----HMQNVSLRELAEKLNIYIGFAAINNFWSLSDEEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENNMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWTKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEDYYLKKQAEICAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIE 341
                            |     | 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       309       319       329       339  
                            |    16                                                                                                                                                                                                                                                                                                                                     
                           15                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:326
 aligned with A5IL00_THEP1 | A5IL00 from UniProtKB/TrEMBL  Length:347

    Alignment length:326
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338      
         A5IL00_THEP1    19 SSQNVSLRELAEKLNIYIGFAAINNFWSLSDEEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENNMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWTKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEDYYLKKQAEICAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIE 344
               SCOP domains d3nj3b_ B: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Glyco_hydro_10-3nj3B01 B:21-336                                                                                                                                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) -----Glyco_hydro_10-3nj3B02 B:21-336                                                                                                                                                                                                                                                                                             ----- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhh..eeeeee..hhhhh.hhhhhhhhhhhhh.eeee....hhhhhh....eeehhhhhhhhhhhhhh..eeeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee..eee....hhhhhhhhhhhhhhh..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..ee...........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nj3 B  16 HMQNVSLRELAEKLNIYIGFAAINNFWSLSDEEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENNMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWTKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEDYYLKKQAEICAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIE 341
                                    25        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       335
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NJ3)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A5IL00_THEP1 | A5IL00)
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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 Related Entries

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        A5IL00_THEP1 | A5IL00: 3niy

(-) Related Entries Specified in the PDB File

3niy NATIVE STRUCTURE