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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NASTURTIUM SEEDLING XYLOGLUCANASE ISOFORM NXG1
 
Authors :  M. J. Baumann, J. Eklof, G. Michel, A. Kallasa, T. T. Teeri, H. Brumer, M. Czjzek
Date :  19 Mar 07  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Glycoside Hydrolase, Xyloglucan-Endo-Transferase, Hydrolase, Glycosidase, Family Gh16, Tropaeolum Majus Xyloglucanase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Baumann, J. Eklof, G. Michel, A. Kallasa, T. T. Teeri, M. Czjzek, H. Brumer
Structural Evidence For The Evolution Of Xyloglucanase Activity From Xyloglucan Endo- Transglycosylases: Biological Implications For Cell Wall Metabolism.
Plant Cell V. 19 1947 2007
PubMed-ID: 17557806  |  Reference-DOI: 10.1105/TPC.107.051391

(-) Compounds

Molecule 1 - CELLULASE
    ChainsA, B, C
    EC Number3.2.1.151, 3.2.1.4
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9-NXG1
    Expression System Taxid4922
    Expression System VectorPGEM T EASY
    FragmentRESIDUES 25-295
    Organism CommonNASTURTIUM
    Organism ScientificTROPAEOLUM MAJUS
    Organism Taxid4020
    SynonymXYLOGLUCAN HYDROLASE
    TissueSEEDLING

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:55 , ARG A:56 , THR A:219 , VAL A:220 , GLU A:221 , THR C:46BINDING SITE FOR RESIDUE GOL A 300
2AC2SOFTWAREILE A:77 , SER A:79 , TYR A:81 , GLU A:94 , GLU A:98 , TRP A:185BINDING SITE FOR RESIDUE GOL A 301
3AC3SOFTWARESER B:79 , GLU B:94 , GLU B:98 , TRP B:185BINDING SITE FOR RESIDUE GOL B 300
4AC4SOFTWARESER C:79 , TYR C:81 , GLU C:94 , GLU C:98 , TRP C:185BINDING SITE FOR RESIDUE GOL C 300

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:218 -A:226
2A:258 -A:271
3B:218 -B:226
4B:258 -B:271
5C:218 -C:226
6C:258 -C:271

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:204 -Pro A:205
2Gln B:204 -Pro B:205
3Gln C:204 -Pro C:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UWA)

(-) 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:274
 aligned with Q07524_TROMA | Q07524 from UniProtKB/TrEMBL  Length:295

    Alignment length:274
                                    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    
         Q07524_TROMA    22 CLGQGPPSPGYYPSSQITSLGFDQGYTNLWGPQHQRVDQGSLTIWLDSTSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDEIDIEFLGTIPGKPYTLQTNVFIEGSGDYNIIGREMRIHLWFDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDATFPLRPLWVYGSVWDASSWATENGKYKADYRYQPFVGKYEDFKLGSCTVEAASSCNPASVSPYGQLSQQQVAAMEWVQKNYMVYNYCDDPTRDHTLTPEC 295
               SCOP domains d2uwaa_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh...hhhhheeeeehhh.eeee..eeeeee.....eeeee...eeeeeeeeeee........eeeeeeee..........eeeeeee........eeeeeee.............eee..........eeeeeee...eeeeee..eeeeeee..hhhhh.....eeeeeeee......hhhh...hhhhh.eeeeeeeeeeeeee..................hhhhhhhhhhhhhhheeee.hhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwa A  -2 AYVQGPPSPGYYPSSQITSLGFDQGYTNLWGPQHQRVDQGSLTIWLDSTSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDEIDIEFLGTIPGKPYTLQTNVFIEGSGDYNIIGREMRIHLWFDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDATFPLRPLWVYGSVWDASSWATENGKYKADYRYQPFVGKYEDFKLGSCTVEAASSCNPASVSPYGQLSQQQVAAMEWVQKNYMVYNYCDDPTRDHTLTPEC 271
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267    

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with Q07524_TROMA | Q07524 from UniProtKB/TrEMBL  Length:295

    Alignment length:274
                                    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    
         Q07524_TROMA    22 CLGQGPPSPGYYPSSQITSLGFDQGYTNLWGPQHQRVDQGSLTIWLDSTSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDEIDIEFLGTIPGKPYTLQTNVFIEGSGDYNIIGREMRIHLWFDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDATFPLRPLWVYGSVWDASSWATENGKYKADYRYQPFVGKYEDFKLGSCTVEAASSCNPASVSPYGQLSQQQVAAMEWVQKNYMVYNYCDDPTRDHTLTPEC 295
               SCOP domains d2uwab_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh...hhhhheeeeehhh.eeee..eeeeee.....eeeee...eeeeeeeeeee........eeeeeeee..........eeeeeee........eeeeeee.............eee..........eeeeeee...eeeeee..eeeeeee..hhhhh.....eeeeeeee.............hhhhh.eeeeeeeeeeeeee..................hhhhhhhhhhhhhhheeee.hhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwa B  -2 AYVQGPPSPGYYPSSQITSLGFDQGYTNLWGPQHQRVDQGSLTIWLDSTSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDEIDIEFLGTIPGKPYTLQTNVFIEGSGDYNIIGREMRIHLWFDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDATFPLRPLWVYGSVWDASSWATENGKYKADYRYQPFVGKYEDFKLGSCTVEAASSCNPASVSPYGQLSQQQVAAMEWVQKNYMVYNYCDDPTRDHTLTPEC 271
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267    

Chain C from PDB  Type:PROTEIN  Length:274
 aligned with Q07524_TROMA | Q07524 from UniProtKB/TrEMBL  Length:295

    Alignment length:274
                                    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    
         Q07524_TROMA    22 CLGQGPPSPGYYPSSQITSLGFDQGYTNLWGPQHQRVDQGSLTIWLDSTSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDEIDIEFLGTIPGKPYTLQTNVFIEGSGDYNIIGREMRIHLWFDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDATFPLRPLWVYGSVWDASSWATENGKYKADYRYQPFVGKYEDFKLGSCTVEAASSCNPASVSPYGQLSQQQVAAMEWVQKNYMVYNYCDDPTRDHTLTPEC 295
               SCOP domains d2uwac_ C: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Glyco_hydro_16-2uwaC01 C:19-203                                                                                                                                                          --------------XET_C-2uwaC04 C:218-271                                Pfam domains (1)
           Pfam domains (2) ---------------------Glyco_hydro_16-2uwaC02 C:19-203                                                                                                                                                          --------------XET_C-2uwaC05 C:218-271                                Pfam domains (2)
           Pfam domains (3) ---------------------Glyco_hydro_16-2uwaC03 C:19-203                                                                                                                                                          --------------XET_C-2uwaC06 C:218-271                                Pfam domains (3)
         Sec.struct. author ...........hhhhhh...hhhhheeeeehhh.eeee..eeeeee.....eeeee...eeeeeeeeeee........eeeeeeee..........eeeeeee........eeeeeee.............eee..........eeeeeeee..eeeeee..eeeeeee..hhhhh.....eeeeeeee.............hhhhh.eeeeeeeeeeeeee..................hhhhhhhhhhhhhhheeee.hhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwa C  -2 AYVQGPPSPGYYPSSQITSLGFDQGYTNLWGPQHQRVDQGSLTIWLDSTSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDEIDIEFLGTIPGKPYTLQTNVFIEGSGDYNIIGREMRIHLWFDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDATFPLRPLWVYGSVWDASSWATENGKYKADYRYQPFVGKYEDFKLGSCTVEAASSCNPASVSPYGQLSQQQVAAMEWVQKNYMVYNYCDDPTRDHTLTPEC 271
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267    

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q07524_TROMA | Q07524)
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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016762    xyloglucan:xyloglucosyl transferase activity    Catalysis of the cleavage of a beta-(1->4) bond in the backbone of a xyloglucan and transfers the xyloglucanyl segment on to O-4 of the non-reducing terminal glucose residue of an acceptor, which can be a xyloglucan or an oligosaccharide of xyloglucan.
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:0042546    cell wall biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall. Includes biosynthesis of constituent macromolecules, such as proteins and polysaccharides, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. A cell wall is the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0006073    cellular glucan metabolic process    The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
    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:0010411    xyloglucan metabolic process    The chemical reactions and pathways involving xyloglucan, the cross-linking glycan composed of (1->4)-beta-D-glucan backbone substituted at regular intervals with beta-D-xylosyl-(1->6) residues, which is present in the primary cell wall of most higher plants.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q07524_TROMA | Q075242uwb 2uwc 2vh9

(-) Related Entries Specified in the PDB File

2uwb CRYSTAL STRUCTURE OF THE NASTURTIUM SEEDLING MUTANT XYLOGLUCANASE ISOFORM NXG1-DELTA-YNIIG
2uwc CRYSTAL STRUCTURE OF NASTURTIUM XYLOGLUCAN HYDROLASE ISOFORM NXG2