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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLAN BETA-1,4-XYLOSIDASE FROM BACILLUS HALODURANS C-125
 
Authors :  A. A. Fedorov, E. V. Fedorov, S. C. Almo, S. K. Burley, New York Sgx Res Center For Structural Genomics (Nysgxrc)
Date :  05 Feb 05  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Nysgxrc Target T1997, Xylosidase, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. A. Fedorov, E. V. Fedorov, S. C. Almo
Crystal Structure Of Xylan Beta-1, 4-Xylosidase From Bacillu Halodurans C-125
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - XYLAN BETA-1,4-XYLOSIDASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificBACILLUS HALODURANS
    Organism Taxid272558
    StrainC-125

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YRZ)

(-) Sites  (0, 0)

(no "Site" information available for 1YRZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asn A:1007 -Pro A:1008
2Phe A:1036 -Pro A:1037
3Gly A:1224 -Pro A:1225
4Tyr A:1232 -Pro A:1233
5Asn B:2007 -Pro B:2008
6Phe B:2036 -Pro B:2037
7Gly B:2224 -Pro B:2225
8Tyr B:2232 -Pro B:2233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YRZ)

(-) 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:522
 aligned with Q9K6P5_BACHD | Q9K6P5 from UniProtKB/TrEMBL  Length:528

    Alignment length:522
                                    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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523  
        Q9K6P5_BACHD      4 RIQNPILPGFHPDPSIVRVGDDYYIATSTFEWFPGVRIHHSRDLKHWRFVSSPLTRTSQLDMKGNMNSGGIWAPCLSYHDGTFYLIYTDVKQWHGAFKDAHNYLVTAQNIEGPWSDPIYLNSSGFDPSLFHDDDGRKWLVNMIWDYRKGNHPFAGIILQEYSEAEQKLVGPVKNIYKGTDIQLTEGPHLYKKDGYYYLLVAEGGTEYEHAATLARSQSIDGPYETDPSYPLVTSTGQPELALQKAGHGSLVETQNGEWYLAHLCGRPLKGKYCTLGRETAIQKVNWTEDGWLRIEDGGNHPLREVTAPDLPEHPFEKEPELDDFDAPQLHHQWNTLRIPADPSWCSLEERPGHLRLRGMESLTSVHSQSLVARRQQSFHCEVETKLEYQPESFQHMAGLVIYYDTEDHVYLHVTWHEEKGKCLQIIQTKGGNYDELLASPIPLAEEKAVYLKGRIHRETMHLYFKQEGEAEWQPVGPTIDVTHMSDDSAKQVRFTGTFVGMATQDLSGTKKPADFDYFRYKE  525
               SCOP domains d1yrza2 A:1004-1320 Beta-D-xylosidase N-terminal domain                                                                                                                                                                                                                                                                      d1yrza1 A:1321-1525 Beta-D-xylosidase C-terminal domain                                                                                                                                                       SCOP domains
               CATH domains 1yrzA01 A:1004-1320 Glycosyl hydrolase domain; family 43                                                                                                                                                                                                                                                                     1yrzA02 A:1321-1525  [code=2.60.120.200, no name defined]                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...........eeeee..eeeeee....ee...eeeee......eeee..................ee...eeeee..eeeeeeeeeee......eeeeeeeee..........ee........eeee.....eeeeeeee........eeeeeeeeee....eeeeeeeeee........eeeeeeee..eeeeeeee.......eeeeeee.......ee......ee.........eeeeeeeeee.....eeeeeeee............eeeeeeeee.....eee.........ee...............ee...........eee........ee.......eeee...........eeeeee....eeeeeeeee.......eeeeeeeeee..eeeeeeeeee...eeeeeeeeee..eeee.....ee......eeeeeeee..eeeeeeee......eeeeeeee.hhh.............eeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1yrz A 1004 RIQNPILPGFHPDPSIVRVGDDYYIATSTFEWFPGVRIHHSRDLKHWRFVSSPLTRTSQLDMKGNMNSGGIWAPCLSYHDGTFYLIYTDVKQWHGAFKDAHNYLVTAQNIEGPWSDPIYLNSSGFDPSLFHDDDGRKWLVNMIWDYRKGNHPFAGIILQEYSEAEQKLVGPVKNIYKGTDIQLTEGPHLYKKDGYYYLLVAEGGTEYEHAATLARSQSIDGPYETDPSYPLVTSTGQPELALQKAGHGSLVETQNGEWYLAHLCGRPLKGKYCTLGRETAIQKVNWTEDGWLRIEDGGNHPLREVTAPDLPEHPFEKEPELDDFDAPQLHHQWNTLRIPADPSWCSLEERPGHLRLRGMESLTSVHSQSLVARRQQSFHCEVETKLEYQPESFQHMAGLVIYYDTEDHVYLHVTWHEEKGKCLQIIQTKGGNYDELLASPIPLAEEKAVYLKGRIHRETMHLYFKQEGEAEWQPVGPTIDVTHMSDDSAKQVRFTGTFVGMATQDLSGTKKPADFDYFRYKE 1525
                                  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      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493      1503      1513      1523  

Chain B from PDB  Type:PROTEIN  Length:522
 aligned with Q9K6P5_BACHD | Q9K6P5 from UniProtKB/TrEMBL  Length:528

    Alignment length:522
                                    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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523  
        Q9K6P5_BACHD      4 RIQNPILPGFHPDPSIVRVGDDYYIATSTFEWFPGVRIHHSRDLKHWRFVSSPLTRTSQLDMKGNMNSGGIWAPCLSYHDGTFYLIYTDVKQWHGAFKDAHNYLVTAQNIEGPWSDPIYLNSSGFDPSLFHDDDGRKWLVNMIWDYRKGNHPFAGIILQEYSEAEQKLVGPVKNIYKGTDIQLTEGPHLYKKDGYYYLLVAEGGTEYEHAATLARSQSIDGPYETDPSYPLVTSTGQPELALQKAGHGSLVETQNGEWYLAHLCGRPLKGKYCTLGRETAIQKVNWTEDGWLRIEDGGNHPLREVTAPDLPEHPFEKEPELDDFDAPQLHHQWNTLRIPADPSWCSLEERPGHLRLRGMESLTSVHSQSLVARRQQSFHCEVETKLEYQPESFQHMAGLVIYYDTEDHVYLHVTWHEEKGKCLQIIQTKGGNYDELLASPIPLAEEKAVYLKGRIHRETMHLYFKQEGEAEWQPVGPTIDVTHMSDDSAKQVRFTGTFVGMATQDLSGTKKPADFDYFRYKE  525
               SCOP domains d1yrzb2 B:2004-2320 Beta-D-xylosidase N-terminal domain                                                                                                                                                                                                                                                                      d1yrzb1 B:2321-2525 Beta-D-xylosidase C-terminal domain                                                                                                                                                       SCOP domains
               CATH domains 1yrzB01 B:2004-2320 Glycosyl hydrolase domain; family 43                                                                                                                                                                                                                                                                     1yrzB02 B:2321-2525  [code=2.60.120.200, no name defined]                                                                                                                                                     CATH domains
           Pfam domains (1) -Glyco_hydro_43-1yrzB01 B:2005-2295                                                                                                                                                                                                                                                                 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -Glyco_hydro_43-1yrzB02 B:2005-2295                                                                                                                                                                                                                                                                 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .ee...........eeeee..eeeeee....ee...eeeee......eeee..................ee...eeeee..eeeeeeeeeee......eeeeeeeee..........ee........eeee.....eeeeeeee........eeeeeeeeee....eeeeeeeeee........eeeeeeee..eeeeeeee.......eeeeeee.......ee......ee.........eeeeeeeeee.....eeeeeeee............eeeeeeeee.....eee.........ee...............ee...........eee........ee.......eeee...........eeeeee....eeeeeeeee.......eeeeeeeeee..eeeeeeeeee...eeeeeeeeee..eeee.....ee......eeeeeeee..eeeeeeee......eeeeeeee.hhh.............eeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1yrz B 2004 RIQNPILPGFHPDPSIVRVGDDYYIATSTFEWFPGVRIHHSRDLKHWRFVSSPLTRTSQLDMKGNMNSGGIWAPCLSYHDGTFYLIYTDVKQWHGAFKDAHNYLVTAQNIEGPWSDPIYLNSSGFDPSLFHDDDGRKWLVNMIWDYRKGNHPFAGIILQEYSEAEQKLVGPVKNIYKGTDIQLTEGPHLYKKDGYYYLLVAEGGTEYEHAATLARSQSIDGPYETDPSYPLVTSTGQPELALQKAGHGSLVETQNGEWYLAHLCGRPLKGKYCTLGRETAIQKVNWTEDGWLRIEDGGNHPLREVTAPDLPEHPFEKEPELDDFDAPQLHHQWNTLRIPADPSWCSLEERPGHLRLRGMESLTSVHSQSLVARRQQSFHCEVETKLEYQPESFQHMAGLVIYYDTEDHVYLHVTWHEEKGKCLQIIQTKGGNYDELLASPIPLAEEKAVYLKGRIHRETMHLYFKQEGEAEWQPVGPTIDVTHMSDDSAKQVRFTGTFVGMATQDLSGTKKPADFDYFRYKE 2525
                                  2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153      2163      2173      2183      2193      2203      2213      2223      2233      2243      2253      2263      2273      2283      2293      2303      2313      2323      2333      2343      2353      2363      2373      2383      2393      2403      2413      2423      2433      2443      2453      2463      2473      2483      2493      2503      2513      2523  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9K6P5_BACHD | Q9K6P5)
molecular function
    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.
    GO:0009044    xylan 1,4-beta-xylosidase activity    Catalysis of the hydrolysis of (1->4)-beta-D-xylans so as to remove successive D-xylose residues from the non-reducing termini.
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.

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    Asn A:1007 - Pro A:1008   [ RasMol ]  
    Asn B:2007 - Pro B:2008   [ RasMol ]  
    Gly A:1224 - Pro A:1225   [ RasMol ]  
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