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(-) Description

Title :  THE HIGH-RESOLUTION CRYSTAL STRUCTURE OF IXT6, A THERMOPHILIC, INTRACELLULAR XYLANASE FROM G. STEAROTHERMOPHILUS
 
Authors :  V. Solomon, A. Teplitsky, G. Golan, R. Gilboa, V. Reiland, S. Shulami, S G. Zolotnitsky, Y. Shoham, G. Shoham
Date :  19 Nov 02  (Deposition) - 25 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Solomon, A. Teplitsky, G. Golan, R. Gilboa, V. Reiland, S. Shulami, S. Moryles, G. Zolotnitsky, Y. Shoham, G. Shoham
The High-Resolution Crystal Structure Of Ixt6, A Thermophilic, Intracellular Xylanase From G. Stearothermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTRA-CELLULAR XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9D
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: XYNA
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: T-6
    Synonym: XYLANASE

 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  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1GOL14Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
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:1015 , ARG B:1282 , ILE B:1285 , GLN B:1286 , HOH B:4208BINDING SITE FOR RESIDUE NA B 402
03AC3SOFTWAREARG A:187 , ASP A:221 , ALA A:225 , HOH A:4135BINDING SITE FOR RESIDUE GOL A 453
04AC4SOFTWAREASP A:65 , LYS A:125 , GOL A:472 , HOH A:4113 , GOL B:464 , CYS B:1113 , HOH B:4449BINDING SITE FOR RESIDUE GOL B 455
05AC5SOFTWAREALA A:13 , ASN A:14 , PHE A:16 , ARG A:17 , GLN A:286BINDING SITE FOR RESIDUE GOL A 461
06AC6SOFTWAREGLY A:124 , LYS A:125 , ILE A:126 , ASP A:169BINDING SITE FOR RESIDUE GOL A 463
07AC7SOFTWAREARG A:120 , ARG A:121 , HOH A:4055 , GOL B:455 , CYS B:1113 , SER B:1116 , ARG B:1120 , HOH B:4048 , HOH B:4163BINDING SITE FOR RESIDUE GOL B 464
08AC8SOFTWARETYR A:166 , PRO A:170 , HOH A:4263 , HOH A:4461 , HOH A:4515BINDING SITE FOR RESIDUE GOL A 465
09AC9SOFTWAREASP B:1138 , ARG B:1145 , TYR B:1179 , ASN B:1180 , LYS B:1186 , HIS B:1250 , ASP B:1251BINDING SITE FOR RESIDUE GOL B 466
10BC1SOFTWAREASN A:2 , LEU A:5 , PRO A:6 , ASP A:36 , HIS A:37 , HOH A:4079 , HOH A:4409BINDING SITE FOR RESIDUE GOL A 467
11BC2SOFTWAREASP A:155 , GLU A:159 , SER A:196 , LEU A:197 , HOH A:4088BINDING SITE FOR RESIDUE GOL A 469
12BC3SOFTWAREGLU A:134 , TYR A:179 , GLN A:210 , HIS A:212 , GLU A:241 , HOH A:4017 , HOH A:4218 , HOH A:4446 , HOH A:4487 , HOH A:4516BINDING SITE FOR RESIDUE GOL A 470
13BC4SOFTWAREASP A:65 , ASP A:69 , HOH A:4038 , HOH A:4131 , HOH A:4517 , GOL B:455 , GOL B:473 , GLU B:1056BINDING SITE FOR RESIDUE GOL A 472
14BC5SOFTWAREGOL A:472 , HOH A:4517 , GLU B:1056 , ARG B:1110 , HOH B:4065 , HOH B:4197 , HOH B:4240 , HOH B:4443BINDING SITE FOR RESIDUE GOL B 473
15BC6SOFTWARETRP B:1085 , GLU B:1134 , GLN B:1210 , HIS B:1212 , GLU B:1241 , ARG B:1252 , TRP B:1291 , HOH B:4090 , HOH B:4529BINDING SITE FOR RESIDUE GOL B 474
16BC7SOFTWAREASP B:1065 , VAL B:1068 , ASP B:1069 , TYR B:1122 , LYS B:1125BINDING SITE FOR RESIDUE GOL A 476

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N82)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1His A:81 -Thr A:82
2Arg A:217 -Pro A:218
3Phe A:303 -Pro A:304
4His B:1081 -Thr B:1082
5Arg B:1217 -Pro B:1218
6Phe B:1303 -Pro B:1304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N82)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N82)

(-) Exons   (0, 0)

(no "Exon" information available for 1N82)

(-) 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: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 d1n82a_ A: Xylanase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1n82A00 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...................hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1n82 A    2 NSSLPSLRDVFANDFRIGAAVNPVTIEMQKQLLIDHVNSITAENHMKFEHLQPEEGKFTFQEADRIVDFACSHRMAVRGHTLVWHNQTPDWVFQDGQGHFVSRDVLLERMKCHISTVVRRYKGKIYCWDVINEAVADEGDELLRPSKWRQIIGDDFMEQAFLYAYEADPDALLFYNDYNECFPEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSLDEIRAAIERYASLGVVLHITELDVSMFEFHDRRTDLAAPTSEMIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRAVSV  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 d1n82b_ B: Xylanase                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1n82B00 B:1004-1331 Glycosidases                                                                                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) ---Glyco_hydro_10-1n82B01 B:1007-1331                                                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ---Glyco_hydro_10-1n82B02 B:1007-1331                                                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ...hhhhhh....eeeeeehhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeeee....hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....eeeeee.............hhhhhhhh.hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh.....eeee..eee....hhhhhhhhhhhhhh...eeeeeeeeee..............hhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh...................hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1n82 B 1004 SLPSLRDVFANDFRIGAAVNPVTIEMQKQLLIDHVNSITAENHMKFEHLQPEEGKFTFQEADRIVDFACSHRMAVRGHTLVWHNQTPDWVFQDGQGHFVSRDVLLERMKCHISTVVRRYKGKIYCWDVINEAVADEGDELLRPSKWRQIIGDDFMEQAFLYAYEADPDALLFYNDYNECFPEKREKIFALVKSLRDKGIPIHGIGMQAHWSLTRPSLDEIRAAIERYASLGVVLHITELDVSMFEFHDRRTDLAAPTSEMIERQAERYGQIFALFKEYRDVIQSVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRAVSV 1331
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323
   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  (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   (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.

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  1n82
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 Related Entries

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        Q09LY9_GEOSE | Q09LY9: 2q8x 3ms8 3msd 3msg 3mua 3mui

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1N82)