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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-XYLOSIDASE (GH31) FROM CELLVIBRIO JAPONICUS
 
Authors :  J. Larsbrink, A. Izumi, F. Ibatullin, A. Nakhai, H. J. Gilbert, G. J. Dav H. Brumer
Date :  26 Oct 10  (Deposition) - 13 Apr 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycosyl Hydrolase Family 31, Beta/Alpha 8 Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Larsbrink, A. Izumi, F. Ibatullin, A. Nakhai, H. J. Gilbert, G. J. Davies, H. Brumer
Structural And Enzymatic Characterisation Of A Glycoside Hydrolase Family 31 Alpha-Xylosidase From Cellvibrio Japonicus Involved In Xyloglucan Saccharification.
Biochem. J. V. 436 567 2011
PubMed-ID: 21426303  |  Reference-DOI: 10.1042/BJ20110299

(-) Compounds

Molecule 1 - ALPHA XYLOSIDASE
    Chains: A
    EC Number: 3.2.1.-
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 155077

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NI2Ligand/IonNICKEL (II) ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:754 , CL A:1991 , CL A:1993 , NI A:1998 , HOH A:2014 , HOH A:2033BINDING SITE FOR RESIDUE CL A1990
02AC2SOFTWAREASN A:503 , GLU A:754 , HIS A:882 , CL A:1990 , CL A:1992 , NI A:1998 , HOH A:2033BINDING SITE FOR RESIDUE CL A1991
03AC3SOFTWAREASN A:503 , CL A:1991 , CL A:1993 , NI A:1998 , HOH A:2033BINDING SITE FOR RESIDUE CL A1992
04AC4SOFTWAREGLU A:885 , CL A:1990 , CL A:1992 , NI A:1998 , HOH A:2014BINDING SITE FOR RESIDUE CL A1993
05AC5SOFTWARETRP A:542 , EDO A:1997BINDING SITE FOR RESIDUE EDO A1994
06AC6SOFTWAREASP A:164BINDING SITE FOR RESIDUE SO4 A1995
07AC7SOFTWAREPHE A:107 , HOH A:2103BINDING SITE FOR RESIDUE EDO A1996
08AC8SOFTWARETRP A:542 , EDO A:1994BINDING SITE FOR RESIDUE EDO A1997
09AC9SOFTWAREASN A:503 , HIS A:882 , CL A:1990 , CL A:1991 , CL A:1992 , CL A:1993 , HOH A:2033BINDING SITE FOR RESIDUE NI A1998
10BC1SOFTWAREHIS A:500 , HOH A:2015 , HOH A:2016 , HOH A:2040BINDING SITE FOR RESIDUE NI A1999

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:442 -Arg A:443
2Glu A:585 -Pro A:586
3Thr A:602 -Pro A:603
4Asn A:743 -Pro A:744

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XVG)

(-) 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:944
 aligned with B3PBD9_CELJU | B3PBD9 from UniProtKB/TrEMBL  Length:988

    Alignment length:945
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         988 
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984   | 
         B3PBD9_CELJU    45 ALAQVERTAEGVVLTLPEGTVKKLRLQVMGERIIRVTALPGTDFGIVPESIQVVAKPATNVPFSVDQAGEKLVLKTSQVSAEVSLLDGTVSFRDAKGNVLLQEENRGTFSPVIHDPDPVDADSYALRQEFNRGSDEGFFGLGQHQNGQVNYAGENVELTTYNLVISIPFLVSSRNYGLLWDNNSITRFGDPREAQPLNQSLKLYDAEGKEGGLTVRYFVGDELKLTRVEADFNHQFYKQGNELENPFPEEVAGAYKNNTLRIELEGSIEAQATGKHQFKMYNSGYAQLSLDGEVVLDRWRMNWNPWYHNFYRELNAGDKHKLKVSWKPDGGFFHLRHLDPLPANEQHELSLASETGKAIDYYFVAGDTKDDIISGYRQLTGKSVMLPKWAYGFWQSRERYKSSDEIIQNLKEYRDRKIPIDNIVLDWSYWPEDAWGSHDFDKQFFPDPKALVDKVHAMNAQIMISVWPKFYPTTDNYKELNAKGFMFNRNLDEKNLDWIGKGYLNAFYDPFSPEATAIFWKQIRDKINVHGFDAWWLDAVEPDIHSNLTFEKRKWLMTPNARGNGAEIFNAYAVPHAEGVYQGELATDGDKRSFILTRSGFGGIQRTGSAIWSGDIVSRWSDMKDQIAAGIGTNLAGVTNWTFDIGGFTPEDRFRHGKKGFVGSWTALDAEQVDEWQELNTRWYQFGAFVPLYRSHGQNPYREIFNIADEGTEVYNAMVWYTKLRYYLMPYIYTLGGDTYHKDGTIMRGLVMDFPNDRKAWDINTQYMFGPAFLVNPVYEYKARSRDVYLPAGSDWYNFYTGEKLAGGQTITADAPLARVPLFVKAGAIVPTGPLIQHVDEGLNSPLLITVYTGANGSFDIYEDDGRSLKYQQGEWSRIPLSYDDVTGTLIIGDRVGSFTGMADERNIRVRFIAGPTADATNFDKAAAEAVTYTGKSVSIKRPR-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PA 14-2xvgA02 A:253-391                                                                                                                    -------------Glyco_hydro_31-2xvgA01 A:405-874                                                                                                                                                                                                                                                                                                                                                                                                                                                      ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeee.......eeeeeeee..eeeeeee...hhhhh................eeeee..eeeee....eeeee.....eeee.....eeee.........................eee.......eeeeee............eee......eeeeeeee...eeeee.....eee......ee....eeee......-.eeeeeee..eeeeeeee...ee.............hhhhhhhhhh..eeeeeeeeeee...eeeeeeeee.eeeeeee...eeeeeee.....eeeeeeeee.....eeeeeeee.....eeeeee..........eeeee.....eeeeeee..hhhhhhhhhhhhhh.....hhhhh.eee......hhhhhhhhhhhhhhh.....eeee.....................hhhhhhhhhhhh..eeeee...ee...hhhhhhhhhh..eehhhhhh............eee...hhhhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhh......eee.....hhhhh.eeee......hhhhhhhhhhhhhhhhh.....ee........hhhhhee..ee..hhhhhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhh..hhhhhhh...eee...eee.........eeeeee....eeee.....eee..eeeeee.......eeee...eeee.....hhhhhh...eeeeee....eeeeeee.....hhhhhh.eeeeeeeee....eeee...eee.......eeeeeeee...............eeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xvg A  45 ALAQVERTAEGVVLTLPEGTVKKLRLQVMGERIIRVTALPGTDFGIVPESIQVVAKPATNVPFSVDQAGEKLVLKTSQVSAEVSLLDGTVSFRDAKGNVLLQEENRGTFSPVIHDPDPVDADSYALRQEFNRGSDEGFFGLGQHQNGQVNYAGENVELTTYNLVISIPFLVSSRNYGLLWDNNSITRFGDPREAQPLNQSLKLYDAEGKE-GLTVRYFVGDELKLTRVEADFNHQFYKQGNELENPFPEEVAGAYKNNTLRIELEGSIEAQATGKHQFKMYNSGYAQLSLDGEVVLDRWRMNWNPWYHNFYRELNAGDKHKLKVSWKPDGGFFHLRHLDPLPANEQHELSLASETGKAIDYYFVAGDTKDDIISGYRQLTGKSVMLPKWAYGFWQSRERYKSSDEIIQNLKEYRDRKIPIDNIVLDWSYWPEDAWGSHDFDKQFFPDPKALVDKVHAMNAQIMISVWPKFYPTTDNYKELNAKGFMFNRNLDEKNLDWIGKGYLNAFYDPFSPEATAIFWKQIRDKINVHGFDAWWLDAVEPDIHSNLTFEKRKWLMTPNARGNGAEIFNAYAVPHAEGVYQGELATDGDKRSFILTRSGFGGIQRTGSAIWSGDIVSRWSDMKDQIAAGIGTNLAGVTNWTFDIGGFTPEDRFRHGKKGFVGSWTALDAEQVDEWQELNTRWYQFGAFVPLYRSHGQNPYREIFNIADEGTEVYNAMVWYTKLRYYLMPYIYTLGGDTYHKDGTIMRGLVMDFPNDRKAWDINTQYMFGPAFLVNPVYEYKARSRDVYLPAGSDWYNFYTGEKLAGGQTITADAPLARVPLFVKAGAIVPTGPLIQHVDEGLNSPLLITVYTGANGSFDIYEDDGRSLKYQQGEWSRIPLSYDDVTGTLIIGDRVGSFTGMADERNIRVRFIAGPTADATNFDKAAAEAVTYTGKSVSIKRPRK 989
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254 |     264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984     
                                                                                                                                                                                                                                           254 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                                                             256
   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  (0, 0)

(no "SCOP Domain" information available for 2XVG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XVG)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: PA14 (11)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B3PBD9_CELJU | B3PBD9)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.

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  2xvg
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 Related Entries

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

UniProtKB/TrEMBL
        B3PBD9_CELJU | B3PBD9: 2xvk 2xvl

(-) Related Entries Specified in the PDB File

2xvk CRYSTAL STRUCTURE OF ALPHA-XYLOSIDASE (GH31) FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH 5 -FLUORO-ALPHA-D-XYLOPYRANOSYL FLUORIDE
2xvl CRYSTAL STRUCTURE OF ALPHA-XYLOSIDASE (GH31) FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH PENTAERYTHRITOL PROPOXYLATE (5 4 PO OH)