Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE HIGH-RESOLUTION CRYSTAL STRUCTURE OF IXT6, A THERMOPHILIC, INTRACELLULAR XYLANASE FROM G. STEAROTHERMOPHILUS
 
Authors :  V. Solomon, A. Teplitsky, R. Gilboa, G. Zolotnitsky, G. Golan, V. Reila S. Moryles, Y. Shoham, G. Shoham
Date :  12 Jun 07  (Deposition) - 20 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase; Xylanase; Intracellular, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Solomon, A. Teplitsky, S. Shulami, G. Zolotnitsky, Y. Shoham, G. Shoham
Structure-Specificity Relationships Of An Intracellular Xylanase From Geobacillus Stearothermophilus
Acta Crystallogr. , Sect. D V. 63 845 2007
PubMed-ID: 17642511  |  Reference-DOI: 10.1107/S0907444907024845

(-) Compounds

Molecule 1 - INTRA-CELLULAR XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D
    Expression System Strain: BL21 (DE3)
    Expression System Vector Type: PLASMID
    Gene: XYNA2
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Strain: BACTERIA T-6
    Synonym: XYLANASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1GOL13Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:15 , ARG A:282 , ILE A:285 , GLN A:286 , HOH A:4002BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWAREASP B:15 , ARG B:282 , ILE B:285 , GLN B:286 , HOH B:4208BINDING SITE FOR RESIDUE NA B 402
03AC3SOFTWAREARG A:187 , ASP A:221 , HOH A:4135 , HOH A:4570BINDING SITE FOR RESIDUE GOL A 453
04AC4SOFTWAREASP A:65 , TYR A:122 , LYS A:125 , HOH A:4113 , CYS B:113 , HOH B:4438 , HOH B:4448BINDING SITE FOR RESIDUE GOL B 455
05AC5SOFTWAREGLY A:124 , LYS A:125 , ILE A:126 , ASP A:169 , HOH A:4541 , HOH A:4740BINDING SITE FOR RESIDUE GOL A 463
06AC6SOFTWAREARG A:120 , ARG A:121 , CYS B:113 , SER B:116 , THR B:117 , ARG B:120 , HOH B:4048 , HOH B:4163 , HOH B:4302 , HOH B:4651BINDING SITE FOR RESIDUE GOL B 464
07AC7SOFTWARETYR A:166 , PRO A:170 , HOH A:4262 , HOH A:4513BINDING SITE FOR RESIDUE GOL A 465
08AC8SOFTWAREASP B:138 , ARG B:145 , TYR B:179 , ASN B:180 , LYS B:186 , HIS B:250 , ASP B:251BINDING SITE FOR RESIDUE GOL B 466
09AC9SOFTWAREASN A:2 , LEU A:5 , PRO A:6 , ASP A:36 , HIS A:37 , HOH A:4079 , HOH A:4408BINDING SITE FOR RESIDUE GOL A 467
10BC1SOFTWAREASP A:155 , GLU A:159 , SER A:196 , LEU A:197 , HOH A:4088BINDING SITE FOR RESIDUE GOL A 469
11BC2SOFTWAREGLU A:134 , TYR A:179 , GLN A:210 , HIS A:212 , GLU A:241 , HOH A:4017 , HOH A:4217 , HOH A:4445 , HOH A:4514 , HOH A:4749BINDING SITE FOR RESIDUE GOL A 470
12BC3SOFTWAREASP A:65 , ASP A:69 , HOH A:4038 , HOH A:4113 , GLU B:56 , HOH B:5007 , HOH B:5008BINDING SITE FOR RESIDUE GOL A 472
13BC4SOFTWARETRP B:85 , GLU B:134 , GLN B:210 , HIS B:212 , GLU B:241 , ARG B:252 , TRP B:291 , HOH B:4090 , HOH B:4526BINDING SITE FOR RESIDUE GOL B 474
14BC5SOFTWAREASP B:65 , ASP B:69 , TYR B:122 , LYS B:125 , HOH B:4603BINDING SITE FOR RESIDUE GOL A 476
15BC6SOFTWAREGLU A:44 , ASN A:45 , LYS A:48 , TRP A:85 , GLN A:88 , TRP A:291 , TRP A:299 , HOH A:4210 , HOH A:4514 , HOH A:4569 , HOH A:4749 , HOH A:4759BINDING SITE FOR RESIDUE GOL A 477

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q8X)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1His A:81 -Thr A:82
2Arg A:217 -Pro A:218
3Phe A:303 -Pro A:304
4His B:81 -Thr B:82
5Arg B:217 -Pro B:218
6Phe B:303 -Pro B:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q8X)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q8X)

(-) 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:330
 aligned with Q09LY9_GEOSE | Q09LY9 from UniProtKB/TrEMBL  Length:331

    Alignment length:330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
         Q09LY9_GEOSE     2 NSSLPSLRDVFANDFRIGAAVNPVTIEMQKQLLIDHVNSITAENHMKFEHLQPEEGKFTFQEADRIVDFACSHRMAVRGHTLVWHNQTPDWVFQDGQGHFVSRDVLLERMKCHISTVVRRYKGKIYCWDVINEAVADEGNELLRPSKWRQIIGDDFMEQAFLYAYEADPDALLFYNDYNECFPEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSLDEIRAAIERYASLGVVLHITELDVSMFEFHDRRTDLAAPTSEMIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRAVSV 331
               SCOP domains d2q8xa_ A: Xylanase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2q8xA00 A:2-331 Glycosidases                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh....eeeeeehhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeeee....hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....eeeeee.............hhhhhhhh.hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh.....eeee..eee....hhhhhhhhhhhhhh...eeeeeeeeee..............hhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh...................hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q8x A   2 NSSLPSLRDVFANDFRIGAAVNPVTIEMQKQLLIDHVNSITAENHMKFEHLQPEEGKFTFQEADRIVDFACSHRMAVRGHTLVWHNQTPDWVFQDGQGHFVSRDVLLERMKCHISTVVRRYKGKIYCWDVINEAVADEGNELLRPSKWRQIIGDDFMEQAFLYAYEADPDALLFYNDYNECFPEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSLDEIRAAIERYASLGVVLHITELDVSMFEFHDRRTDLAAPTSEMIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRAVSV 331
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with Q09LY9_GEOSE | Q09LY9 from UniProtKB/TrEMBL  Length:331

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
         Q09LY9_GEOSE     4 SLPSLRDVFANDFRIGAAVNPVTIEMQKQLLIDHVNSITAENHMKFEHLQPEEGKFTFQEADRIVDFACSHRMAVRGHTLVWHNQTPDWVFQDGQGHFVSRDVLLERMKCHISTVVRRYKGKIYCWDVINEAVADEGNELLRPSKWRQIIGDDFMEQAFLYAYEADPDALLFYNDYNECFPEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSLDEIRAAIERYASLGVVLHITELDVSMFEFHDRRTDLAAPTSEMIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRAVSV 331
               SCOP domains d2q8xb_ B: Xylanase                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2q8xB00 B:4-331 Glycosidases                                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ---Glyco_hydro_10-2q8xB01 B:7-331                                                                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) ---Glyco_hydro_10-2q8xB02 B:7-331                                                                                                                                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author ...hhhhhh....eeeeeehhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeeee....hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....eeeeee.............hhhhhhhh.hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh.....eeee..ee.....hhhhhhhhhhhhhh...eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh...................hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8x B   4 SLPSLRDVFANDFRIGAAVNPVTIEMQKQLLIDHVNSITAENHMKFEHLQPEEGKFTFQEADRIVDFACSHRMAVRGHTLVWHNQTPDWVFQDGQGHFVSRDVLLERMKCHISTVVRRYKGKIYCWDVINEAVADEGNELLRPSKWRQIIGDDFMEQAFLYAYEADPDALLFYNDYNECFPEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSLDEIRAAIERYASLGVVLHITELDVSMFEFHDRRTDLAAPTSEMIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRAVSV 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q09LY9_GEOSE | Q09LY9)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:217 - Pro A:218   [ RasMol ]  
    Arg B:217 - Pro B:218   [ RasMol ]  
    His A:81 - Thr A:82   [ RasMol ]  
    His B:81 - Thr B:82   [ RasMol ]  
    Phe A:303 - Pro A:304   [ RasMol ]  
    Phe B:303 - Pro B:304   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2q8x
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q09LY9_GEOSE | Q09LY9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.8
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q09LY9_GEOSE | Q09LY9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q09LY9_GEOSE | Q09LY9: 1n82 3ms8 3msd 3msg 3mua 3mui

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q8X)