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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPLEX XYLANASE 10B FROM THERMOTOGA MARITIMA WITH XYLOBIOSE
 
Authors :  Ihsanawati, T. Kumasaka, T. Kaneko, S. Nakamura, N. Tanaka
Date :  02 Mar 04  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Xylanase 10B, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Ihsanawati, T. Kumasaka, T. Kaneko, C. Morokuma, R. Yatsunami, T. Sato, S. Nakamura, N. Tanaka
Structural Basis Of The Substrate Subsite And The Highly Thermal Stability Of Xylanase 10B From Thermotoga Maritima Msb8
Proteins V. 61 999 2005
PubMed-ID: 16247799  |  Reference-DOI: 10.1002/PROT.20700
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE B
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: XYLANASE, XYLANASE 10B

 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
1ACY6Ligand/IonACETIC ACID
2XYP2Ligand/IonBETA-D-XYLOPYRANOSE
3XYS2Ligand/IonXYLOPYRANOSE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE
3XYS1Ligand/IonXYLOPYRANOSE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE
3XYS1Ligand/IonXYLOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREXYP A:2 , GLU A:561 , ASN A:562 , GLN A:605 , TRP A:794 , TRP A:802 , HOH A:1168 , HOH A:1171BINDING SITE FOR RESIDUE XYS A 1
02AC2SOFTWAREXYS A:1 , LYS A:565 , HIS A:598 , ASN A:646 , GLU A:647 , GLN A:722 , GLU A:753 , TRP A:794 , TRP A:802 , HOH A:984 , HOH A:1173BINDING SITE FOR RESIDUE XYP A 2
03AC3SOFTWAREXYP B:4 , GLU B:561 , ASN B:562 , GLN B:605 , TRP B:794 , TRP B:802BINDING SITE FOR RESIDUE XYS B 3
04AC4SOFTWAREACY B:2 , XYS B:3 , LYS B:565 , HIS B:598 , ASN B:646 , GLU B:647 , GLN B:722 , GLU B:753 , TRP B:794 , TRP B:802BINDING SITE FOR RESIDUE XYP B 4
05AC5SOFTWAREARG A:575 , ASN A:577 , HOH A:1087 , ARG B:575BINDING SITE FOR RESIDUE ACY A 842
06AC6SOFTWAREXYP B:4 , TYR B:690BINDING SITE FOR RESIDUE ACY B 2
07AC7SOFTWARELYS A:744 , HOH A:1165 , GLY B:608BINDING SITE FOR RESIDUE ACY A 3
08AC8SOFTWAREHOH A:1108 , HOH B:875 , HOH B:876BINDING SITE FOR RESIDUE ACY B 842
09AC9SOFTWAREHOH A:1083 , ARG B:736 , LYS B:777 , HOH B:990BINDING SITE FOR RESIDUE ACY A 5
10BC1SOFTWARESER A:542 , LYS A:799 , HOH A:963 , LYS B:712BINDING SITE FOR RESIDUE ACY A 6

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:598 -Thr A:599
2His B:598 -Thr B:599

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VBR)

(-) Exons   (0, 0)

(no "Exon" information available for 1VBR)

(-) 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:324
 aligned with Q9WXS5_THEMA | Q9WXS5 from UniProtKB/TrEMBL  Length:347

    Alignment length:324
                                    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    
         Q9WXS5_THEMA    23 VSLRELAEKLNIYIGFAAINNFWSLSDAEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENDMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWAKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEEYYLKKQAEVCAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIEER 346
               SCOP domains d1vbra1 A:517-840 Xylanase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1vbrA00 A:517-840 Glycosidases                                                                                                                                                                                                                                                                                                       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....hhhhhhhhhhhhhh...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..ee...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vbr A 517 VSLRELAEKLNIYIGFAAINNFWSLSDAEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENDMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWAKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEEYYLKKQAEVCAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIEER 840
                                   526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836    


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q9WXS5_THEMA | Q9WXS5 from UniProtKB/TrEMBL  Length:347

    Alignment length:324
                                    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    
         Q9WXS5_THEMA    23 VSLRELAEKLNIYIGFAAINNFWSLSDAEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENDMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWAKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEEYYLKKQAEVCAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIEER 346
               SCOP domains d1vbrb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vbrB00 B:517-840 Glycosidases                                                                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -Glyco_hydro_10-1vbrB01 B:518-833                                                                                                                                                                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) -Glyco_hydro_10-1vbrB02 B:518-833                                                                                                                                                                                                                                                                                            ------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhh..eeeeee..hhhhh.hhhhhhhhhhhhh.eeee....hhhhhh....eeehhhhhhhhhhhhhh..eeeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee..eee....hhhhhhhhhhhhhh...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..ee...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vbr B 517 VSLRELAEKLNIYIGFAAINNFWSLSDAEKYMEVARREFNILTPENQMKWDTIHPERDRYNFTPAEKHVEFAEENDMIVHGHTLVWHNQLPGWITGREWTKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDSGTYRESVWYKTIGPEYIEKAFRWAKEADPDAILIYNDYSIEEINAKSNFVYNMIKELKEKGVPVDGIGFQMHIDYRGLNYDSFRRNLERFAKLGLQIYITEMDVRIPLSGSEEYYLKKQAEVCAKIFDICLDNPAVKAIQFWGFTDKYSWVPGFFKGYGKALLFDENYNPKPCYYAIKEVLEKKIEER 840
                                   526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9WXS5_THEMA | Q9WXS5)
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

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

UniProtKB/TrEMBL
        Q9WXS5_THEMA | Q9WXS5: 1vbu

(-) Related Entries Specified in the PDB File

1vbu NATIVE XYLANASE 10B