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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-XYLOSIDASE (GH31) FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH PENTAERYTHRITOL PROPOXYLATE (5 4 PO OH)
 
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 :  2.30
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, PUTATIVE, XYL31A
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-DEST42
    Expression System Vector Type: PLASMID
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 155077
    Synonym: ALPHA XYLOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2NI3Ligand/IonNICKEL (II) ION
3PXN1Ligand/Ion(2S)-1-[3-{[(2R)-2-HYDROXYPROPYL]OXY}-2,2-BIS({[(2R)-2-HYDROXYPROPYL]OXY}METHYL)PROPOXY]PROPAN-2-OL
4SO43Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:882 , CL A:1996 , CL A:1997 , CL A:1998 , CL A:1999 , CL A:2000BINDING SITE FOR RESIDUE NI A1989
02AC2SOFTWAREHIS A:500 , CL A:2002 , HOH A:2048 , HOH A:2119 , HOH A:2121 , HOH A:2325BINDING SITE FOR RESIDUE NI A1990
03AC3SOFTWAREHIS A:700 , HOH A:2058 , HOH A:2176 , HOH A:2177 , HOH A:2489BINDING SITE FOR RESIDUE NI A1991
04AC4SOFTWAREGLU A:847BINDING SITE FOR RESIDUE SO4 A1992
05AC5SOFTWAREHIS A:158 , GLU A:237BINDING SITE FOR RESIDUE SO4 A1993
06AC6SOFTWAREASP A:164 , LYS A:401 , GLU A:611 , HOH A:2442BINDING SITE FOR RESIDUE SO4 A1994
07AC7SOFTWARELYS A:461BINDING SITE FOR RESIDUE CL A1995
08AC8SOFTWAREASN A:503 , NI A:1989 , CL A:1997 , CL A:1999 , CL A:2000BINDING SITE FOR RESIDUE CL A1996
09AC9SOFTWAREGLN A:881 , GLU A:885 , NI A:1989 , CL A:1996 , CL A:1998 , CL A:1999BINDING SITE FOR RESIDUE CL A1997
10BC1SOFTWAREGLU A:754 , GLU A:885 , NI A:1989 , CL A:1997 , CL A:1999 , CL A:2000 , HOH A:2111BINDING SITE FOR RESIDUE CL A1998
11BC2SOFTWAREASP A:459 , NI A:1989 , CL A:1996 , CL A:1997 , CL A:1998 , CL A:2000 , HOH A:2111BINDING SITE FOR RESIDUE CL A1999
12BC3SOFTWAREASN A:503 , GLU A:754 , HIS A:882 , NI A:1989 , CL A:1996 , CL A:1998 , CL A:1999BINDING SITE FOR RESIDUE CL A2000
13BC4SOFTWARENI A:1990 , HOH A:2048 , HOH A:2119 , HOH A:2121 , HOH A:2325BINDING SITE FOR RESIDUE CL A2002
14BC5SOFTWARETRP A:347 , TRP A:471 , TRP A:542 , SER A:590 , HOH A:2300 , HOH A:2421 , HOH A:2471 , HOH A:2523 , HOH A:2714BINDING SITE FOR RESIDUE PXN A2001

(-) SS Bonds  (0, 0)

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

(-) 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 2XVL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XVL)

(-) 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:944
                                    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 988
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PA14-2xvlA02 A:253-391                                                                                                                     -------------Glyco_hydro_31-2xvlA01 A:405-874                                                                                                                                                                                                                                                                                                                                                                                                                                                      ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeee.......eeeeeeee..eeeeeee...hhhhh................eeeee..eeeee...eeeeee.....eeeee....eeee.....eee.............eeeeeee.......eeeeee............eee......eeeeeeee...eeeee.....eee......ee....eeee........eeeeeee..eeeeeeee...ee..eee..ee.......hhhhhhh..eeeeeeeeeee...eeeeeeeee.eeeeeee..eeeeeeee.....eeeeeeeee....eeeeeeeee.....eeeeee...hhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhh.....hhhhh.eee......hhhhhhhhhhhhhhh.....eeee.....................hhhhhhhhhhhh..eeeeee..ee...hhhhhhhhhh..eehhhhhh............eee...hhhhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhh.......hhhhhh..hhhhhhhhhhhhhhhhh......eee.....hhhhh.eeee......hhhhhhhhhhhhhhhhhh....ee........hhhhhee..ee..hhhhhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhh..hhhhhhh...eee...eee.........eeeeee.....eee.....ee...eeeeee.......eeee...eeee.....hhhhhh...eeeeee....eeeeeee.....hhhhhh.eeeeeeeee....eeee...eee.......eeeeeeee...............eeeee....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xvl A  45 ALAQVERTAEGVVLTLPEGTVKKLRLQVMGERIIRVTALPGTDFGIVPESIQVVAKPATNVPFSVDQAGEKLVLKTSQVSAEVSLLDGTVSFRDAKGNVLLQEENRGTFSPVIHDPDPVDADSYALRQEFNRGSDEGFFGLGQHQNGQVNYAGENVELTTYNLVISIPFLVSSRNYGLLWDNNSITRFGDPREAQPLNQSLKLYDAEGKEGGLTVRYFVGDELKLTRVEADFNHQFYKQGNELENPFPEEVAGAYKNNTLRIELEGSIEAQATGKHQFKMYNSGYAQLSLDGEVVLDRWRMNWNPWYHNFYRELNAGDKHKLKVSWKPDGGFFHLRHLDPLPANEQHELSLASETGKAIDYYFVAGDTKDDIISGYRQLTGKSVMLPKWAYGFWQSRERYKSSDEIIQNLKEYRDRKIPIDNIVLDWSYWPEDAWGSHDFDKQFFPDPKALVDKVHAMNAQIMISVWPKFYPTTDNYKELNAKGFMFNRNLDEKNLDWIGKGYLNAFYDPFSPEATAIFWKQIRDKINVHGFDAWWLDAVEPDIHSNLTFEKRKWLMTPNARGNGAEIFNAYAVPHAEGVYQGELATDGDKRSFILTRSGFGGIQRTGSAIWSGDIVSRWSDMKDQIAAGIGTNLAGVTNWTFDIGGFTPEDRFRHGKKGFVGSWTALDAEQVDEWQELNTRWYQFGAFVPLYRSHGQNPYREIFNIADEGTEVYNAMVWYTKLRYYLMPYIYTLGGDTYHKDGTIMRGLVMDFPNDRKAWDINTQYMFGPAFLVNPVYEYKARSRDVYLPAGSDWYNFYTGEKLAGGQTITADAPLARVPLFVKAGAIVPTGPLIQHVDEGLNSPLLITVYTGANGSFDIYEDDGRSLKYQQGEWSRIPLSYDDVTGTLIIGDRVGSFTGMADERNIRVRFIAGPTADATNFDKAAAEAVTYTGKSVSIKRPR 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
   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 2XVL)

(-) CATH Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        B3PBD9_CELJU | B3PBD9: 2xvg 2xvk

(-) Related Entries Specified in the PDB File

2xvg CRYSTAL STRUCTURE OF ALPHA-XYLOSIDASE (GH31) FROM CELLVIBRIO JAPONICUS
2xvk CRYSTAL STRUCTURE OF ALPHA-XYLOSIDASE (GH31) FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH 5 -FLUORO-ALPHA-D-XYLOPYRANOSYL FLUORIDE