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(-) Description

Title :  CRYSTAL STRUCTURE OF A CELL-WALL INVERTASE FROM ARABIDOPSIS THALIANA
 
Authors :  M. Verhaest, K. Le Roy, C. De Ranter, A. Van Laere, W. Van Den Ende, A
Date :  18 Jul 05  (Deposition) - 29 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Five Fold Beta Propeller, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Verhaest, W. Lammens, K. Le Roy, B. De Coninck, C. J. De Ranter, A. Van Laere, W. Van Den Ende, A. Rabijns
X-Ray Diffraction Structure Of A Cell-Wall Invertase From Arabidopsis Thaliana.
Acta Crystallogr. , Sect. D V. 62 1555 2006
PubMed-ID: 17139091  |  Reference-DOI: 10.1107/S0907444906044489

(-) Compounds

Molecule 1 - INVERTASE
    Chains: A
    EC Number: 3.2.1.26
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Gene: AT3G13790
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: BETA-FRUCTOFURANOSIDASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MAN5Ligand/IonALPHA-D-MANNOSE
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:242 , LYS A:277 , ASN A:299 , GLU A:300 , SER A:301 , ASP A:461 , NAG A:751 , HOH A:1001 , HOH A:1043 , HOH A:1066 , HOH A:1083BINDING SITE FOR RESIDUE NAG A 750
02AC2SOFTWAREASP A:461 , THR A:463 , TYR A:522 , NAG A:750 , MAN A:752 , MAN A:758 , HOH A:1023 , HOH A:1066 , HOH A:1099BINDING SITE FOR RESIDUE NAG A 751
03AC3SOFTWARETHR A:463 , NAG A:751 , MAN A:753 , MAN A:754BINDING SITE FOR RESIDUE MAN A 752
04AC4SOFTWAREGLN A:396 , SER A:400 , MAN A:752 , MAN A:759 , HOH A:1124 , HOH A:1371BINDING SITE FOR RESIDUE MAN A 753
05AC5SOFTWARELYS A:384 , MAN A:752 , MAN A:758BINDING SITE FOR RESIDUE MAN A 754
06AC6SOFTWARETYR A:522 , GLN A:523 , NAG A:751 , MAN A:754 , HOH A:1350BINDING SITE FOR RESIDUE MAN A 758
07AC7SOFTWARELYS A:401 , MAN A:753 , HOH A:1244BINDING SITE FOR RESIDUE MAN A 759
08AC8SOFTWAREASN A:116 , SER A:118 , ASP A:119 , ARG A:123BINDING SITE FOR RESIDUE NAG A 770
09AC9SOFTWAREASN A:143 , SER A:145 , SER A:146 , LYS A:168 , ILE A:169 , HIS A:170 , NAG A:791 , HOH A:1257BINDING SITE FOR RESIDUE NAG A 790
10BC1SOFTWARENAG A:790 , HOH A:1362BINDING SITE FOR RESIDUE NAG A 791
11BC2SOFTWAREASN A:22 , ASP A:23 , GLN A:39 , TRP A:47 , TRP A:82 , SER A:83 , ASP A:149 , GLU A:203BINDING SITE FOR RESIDUE GOL A 1760
12BC3SOFTWARETRP A:47 , TRP A:82BINDING SITE FOR RESIDUE GOL A 1761
13BC4SOFTWARELEU A:117 , SER A:118 , GLY A:214 , SER A:215 , ASN A:216 , HOH A:1292BINDING SITE FOR RESIDUE GOL A 1762
14BC5SOFTWARETRP A:334 , ARG A:337 , GLU A:340 , ARG A:343 , GLU A:374 , TRP A:533 , HOH A:1370BINDING SITE FOR RESIDUE GOL A 1763

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:399 -A:448

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:131 -Pro A:132
2Gly A:411 -Pro A:412

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AC1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F32PS00609 Glycosyl hydrolases family 32 active site.INV1_ARATH56-69  1A:13-26

(-) Exons   (0, 0)

(no "Exon" information available for 2AC1)

(-) 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:537
 aligned with INV1_ARATH | Q43866 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:537
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       
           INV1_ARATH    48 NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS 584
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2ac1A02 A:344-535 Exo-inulinase; domain 1                                                                                                                                                       ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeeeeee..eeeeeeee..........eeeeeee......eeeeeee...hhhhh..eeeeeeee.....eeeeeeee.....eeeeeeee..........eee...................ee.....ee.....eeeeeeeee..eeeeeeeee......ee.....eeee....eeeeeeeeee..................eeeeeeeee.....eeeeeeeee....eeee..................eeeeeeee....eeeeeeee....hhhhhhhhhee.ee...eeeee......eeeee.hhhhhhh....eeeeeeee...eeee.......eeeeeeeee..hhhhhee......hhhhhhhhh.......eeeeeeeeee.......eeeeeeeee.......eeeeeeee..............eeeee.......eeeeeeee..eeeeee....eeeeee......hhhhheeeeee.....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------GLYCOSYL_HYDRO----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ac1 A   5 NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS 541
                                    14        24        34        44        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
   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 2AC1)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AC1)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (INV1_ARATH | Q43866)
molecular function
    GO:0004564    beta-fructofuranosidase activity    Catalysis of the reaction: a fructofuranosylated fructofuranosyl acceptor + H2O = a non fructofuranosylated fructofuranosyl acceptor + a beta-D-fructofuranoside.
    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:0004575    sucrose alpha-glucosidase activity    Catalysis of the reaction: sucrose + H2O = alpha-D-glucose + beta-D-fructose.
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:0080167    response to karrikin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a karrikin stimulus. Karrikins are signaling molecules in smoke from burning vegetation that trigger seed germination for many angiosperms (flowering plants).
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
cellular component
    GO:0048046    apoplast    The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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UniProtKB/Swiss-Prot
        INV1_ARATH | Q43866: 2oxb 2qqu 2qqv 2qqw 2xqr

(-) Related Entries Specified in the PDB File

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