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(-) Description

Title :  XYLOGLUCAN ENDOTRANSGLYCOSYLASE IN COMPLEX WITH THE XYLOGLUCAN NONASACCHARIDE XLLG.
 
Authors :  P. Johansson, H. Brumer, A. M. Kallas, H. Henriksson, S. E. Denman, T. T. Teeri, T. A. Jones
Date :  03 Sep 03  (Deposition) - 18 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase, Xet, Xth, Xeh, Transglycosylation, Xyloglucan, Transferase, Glycosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Johansson, H. Brumer, M. J. Baumann, A. M. Kallas, H. Henriksson, S. E. Denman, T. T. Teeri, T. A. Jones
Crystal Structures Of A Poplar Xyloglucan Endotransglycosylase Reveal Details Of Transglycosylation Acceptor Binding
Plant Cell V. 16 874 2004
PubMed-ID: 15020748  |  Reference-DOI: 10.1105/TPC.020065

(-) Compounds

Molecule 1 - XYLOGLUCAN ENDOTRANSGLYCOSYLASE
    Chains: A, B
    EC Number: 2.4.1.207
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Expression System Vector: PPIC9
    Organism Common: EUROPEAN ASPEN
    Organism Scientific: POPULUS TREMULA
    Organism Taxid: 113636

 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  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2BMA2Ligand/IonBETA-D-MANNOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5XYS4Ligand/IonXYLOPYRANOSE
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5XYS2Ligand/IonXYLOPYRANOSE
Biological Unit 2 (5, 9)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5XYS2Ligand/IonXYLOPYRANOSE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:91 , GLY A:92 , ASN A:93 , GLN A:97 , PRO A:98 , ILE A:100 , TYR A:118 , ALA A:180 , THR A:181 , ARG A:182 , NAG A:1274 , HOH A:2108 , HOH A:2109BINDING SITE FOR RESIDUE NAG A1273
02AC2SOFTWARETYR A:118 , ARG A:182 , NAG A:1273 , BMA A:1275 , HOH A:2108 , HOH A:2110BINDING SITE FOR RESIDUE NAG A1274
03AC3SOFTWARENAG A:1274BINDING SITE FOR RESIDUE BMA A1275
04AC4SOFTWAREASP A:87 , GLU A:89 , GLN A:102 , ASN A:104 , GLU A:114 , BGC A:1277 , XYS A:1279 , HOH A:2111BINDING SITE FOR RESIDUE BGC A1276
05AC5SOFTWAREGLU A:114 , ARG A:116 , TRP A:179 , BGC A:1276 , BGC A:1278 , XYS A:1279 , XYS A:1280 , GAL A:1281BINDING SITE FOR RESIDUE BGC A1277
06AC6SOFTWARETRP A:179 , GLY A:183 , BGC A:1277 , XYS A:1280 , HOH A:2082BINDING SITE FOR RESIDUE BGC A1278
07AC7SOFTWAREASP A:178 , TRP A:179 , BGC A:1276 , BGC A:1277BINDING SITE FOR RESIDUE XYS A1279
08AC8SOFTWAREGLU A:114 , BGC A:1277 , BGC A:1278 , GAL A:1281BINDING SITE FOR RESIDUE XYS A1280
09AC9SOFTWAREASP A:112 , GLU A:114 , ARG A:258 , BGC A:1277 , XYS A:1280 , HOH A:2057BINDING SITE FOR RESIDUE GAL A1281
10BC1SOFTWARELEU B:91 , GLY B:92 , ASN B:93 , GLN B:97 , PRO B:98 , ILE B:100 , TYR B:118 , ALA B:180 , THR B:181 , ARG B:182 , NAG B:1274 , HOH B:2041 , HOH B:2127 , HOH B:2128BINDING SITE FOR RESIDUE NAG B1273
11BC2SOFTWARETYR B:118 , ARG B:182 , ILE B:249 , NAG B:1273 , BMA B:1275 , HOH B:2112 , HOH B:2127 , HOH B:2128 , HOH B:2129BINDING SITE FOR RESIDUE NAG B1274
12BC3SOFTWARENAG B:1274BINDING SITE FOR RESIDUE BMA B1275
13BC4SOFTWAREGLU B:89 , GLN B:102 , ASN B:104 , GLU B:114 , TRP B:179 , BGC B:1277 , XYS B:1279 , HOH B:2130BINDING SITE FOR RESIDUE BGC B1276
14BC5SOFTWAREGLU B:114 , ARG B:116 , TRP B:179 , BGC B:1276 , BGC B:1278 , XYS B:1279 , XYS B:1280 , GAL B:1281BINDING SITE FOR RESIDUE BGC B1277
15BC6SOFTWARETRP B:179 , GLY B:183 , BGC B:1277 , XYS B:1280 , GAL B:1281 , HOH B:2078BINDING SITE FOR RESIDUE BGC B1278
16BC7SOFTWARETRP B:174 , ASP B:178 , TRP B:179 , BGC B:1276 , BGC B:1277 , HOH B:2131BINDING SITE FOR RESIDUE XYS B1279
17BC8SOFTWAREGLU B:114 , ARG B:116 , BGC B:1277 , BGC B:1278 , GAL B:1281 , HOH B:2132 , HOH B:2133BINDING SITE FOR RESIDUE XYS B1280
18BC9SOFTWAREASP B:112 , GLU B:114 , ARG B:258 , BGC B:1277 , BGC B:1278 , XYS B:1280 , HOH B:2134BINDING SITE FOR RESIDUE GAL B1281

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:207 -A:216
2A:253 -A:266
3B:253 -B:266

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:193 -Pro A:194
2Ala B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UMZ)

(-) 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:267
 aligned with Q8GZD5_9ROSI | Q8GZD5 from UniProtKB/TrEMBL  Length:294

    Alignment length:267
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
         Q8GZD5_9ROSI    28 PVDVAFGRNYVPTWAFDHIKYFNGGNEIQLHLDKYTGTGFQSKGSYLFGHFSMQMKLVPGDSAGTVTAFYLSSQNSEHDEIDFEFLGNRTGQPYILQTNVFTGGKGDREQRIYLWFDPTKEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKDLGVKFPFNQPMKIYSSLWNADDWATRGGLEKTDWSKAPFIASYRSFHIDGCEASVEAKFCATQGARWWDQKEFQDLDAFQYRRLSWVRQKYTIYNYCTDRSRYPSMPPECKRDRDI 294
               SCOP domains d1umza_ A: Xyloglucan endotransglycosylase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1umzA00 A:6-272  [code=2.60.120.200, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeehhh.eeeehhh.eeeeee.....eeeee...eeeeeeeeeee........eeeeeeee.......eeeeeee........eeeeeee........eee..........eeeeeee...eeeeee..eeeeeee.hhhhh.........eeeeeeee.....hhhhh...hhhhh.eeeeeeeeeeeeee.............hhhhhhhhh..hhhhhhhhhhhhhhheeee.hhh........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1umz A   6 PVDVAFGRNYVPTWAFDHIKYFNGGNEIQLHLDKYTGTGFQSKGSYLFGHFSMQMKLVPGDSAGTVTAFYLSSQNSEHDEIDFEFLGNRTGQPYILQTNVFTGGKGDREQRIYLWFDPTKEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKDLGVKFPFNQPMKIYSSLWNADDWATRGGLEKTDWSKAPFIASYRSFHIDGCEASVEAKFCATQGARWWDQKEFQDLDAFQYRRLSWVRQKYTIYNYCTDRSRYPSMPPECKRDRDI 272
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with Q8GZD5_9ROSI | Q8GZD5 from UniProtKB/TrEMBL  Length:294

    Alignment length:264
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
         Q8GZD5_9ROSI    31 VAFGRNYVPTWAFDHIKYFNGGNEIQLHLDKYTGTGFQSKGSYLFGHFSMQMKLVPGDSAGTVTAFYLSSQNSEHDEIDFEFLGNRTGQPYILQTNVFTGGKGDREQRIYLWFDPTKEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKDLGVKFPFNQPMKIYSSLWNADDWATRGGLEKTDWSKAPFIASYRSFHIDGCEASVEAKFCATQGARWWDQKEFQDLDAFQYRRLSWVRQKYTIYNYCTDRSRYPSMPPECKRDRDI 294
               SCOP domains d1umzb_ B: Xyloglucan endotransglycosylase                                                                                                                                                                                                                               SCOP domains
               CATH domains 1umzB00 B:9-272  [code=2.60.120.200, no name defined]                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) --Glyco_hydro_16-1umzB01 B:11-192                                                                                                                                                       -----------------------XET_C-1umzB03 B:216-266                            ------ Pfam domains (1)
           Pfam domains (2) --Glyco_hydro_16-1umzB02 B:11-192                                                                                                                                                       -----------------------XET_C-1umzB04 B:216-266                            ------ Pfam domains (2)
         Sec.struct. author .hhhhheeeeehhh.eeee....eeeeee.....eeeee...eeeeeeeeeee........eeeeeeee.......eeeeeee........eeeeeee........eee..........eeeeeee...eeeeee..eeeeeee.hhhhh.........eeeeeeee.....hhhhh...hhhhh.eeeeeeeeeeeeee.............hhhhhhhhh..hhhhhhhhhhhhhhheeee.hhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1umz B   9 VAFGRNYVPTWAFDHIKYFNGGNEIQLHLDKYTGTGFQSKGSYLFGHFSMQMKLVPGDSAGTVTAFYLSSQNSEHDEIDFEFLGNRTGQPYILQTNVFTGGKGDREQRIYLWFDPTKEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKDLGVKFPFNQPMKIYSSLWNADDWATRGGLEKTDWSKAPFIASYRSFHIDGCEASVEAKFCATQGARWWDQKEFQDLDAFQYRRLSWVRQKYTIYNYCTDRSRYPSMPPECKRDRDI 272
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Concanavalin (293)
(-)
Clan: no clan defined [family: XET_C] (6)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8GZD5_9ROSI | Q8GZD5)
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:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    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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        Q8GZD5_9ROSI | Q8GZD5: 1un1

(-) Related Entries Specified in the PDB File

1un1 XYLOGLUCAN ENDOTRANSGLYCOSYLASE NATIVE STRUCTURE