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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PECTIN METHYLESTERASE AND ITS INHIBITOR PROTEIN
 
Authors :  A. Di Matteo, A. Raiola, L. Camardella, A. Giovane, D. Bonivento, G. De Lorenzo, F. Cervone, D. Bellincampi, D. Tsernoglou
Date :  16 Sep 04  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, Beta Helix, Four Helix Bundle, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Di Matteo, A. Giovane, A. Raiola, L. Camardella, D. Bonivento, G. De Lorenzo, F. Cervone, D. Bellincampi, D. Tsernoglou
Structural Basis For The Interaction Between Pectin Methylesterase And A Specific Inhibitor Protein
Plant Cell V. 17 849 2005
PubMed-ID: 15722470  |  Reference-DOI: 10.1105/TPC.104.028886
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTINESTERASE 1
    ChainsA
    EC Number3.1.1.11
    Organism ScientificSOLANUM LYCOPERSICUM
    Organism Taxid4081
    SynonymPECTIN METHYLESTERASE 1, PE 1
    TissuePERICARP
 
Molecule 2 - PECTINESTERASE INHIBITOR
    ChainsB
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZALPHAA
    Expression System StrainX-33
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    Organism ScientificACTINIDIA CHINENSIS
    Organism Taxid3625
    SynonymPECTIN METHYLESTERASE INHIBITOR, PMEI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XG2)

(-) Sites  (0, 0)

(no "Site" information available for 1XG2)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:9 -B:18
2B:74 -B:114

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro B:121 -Pro B:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XG2)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PECTINESTERASE_1PS00800 Pectinesterase signature 1.PME1_SOLLC258-277  1A:29-48
2PECTINESTERASE_2PS00503 Pectinesterase signature 2.PME1_SOLLC377-386  1A:148-157

(-) Exons   (0, 0)

(no "Exon" information available for 1XG2)

(-) 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:317
 aligned with PME1_SOLLC | P14280 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:317
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       
           PME1_SOLLC   230 IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVAYVDGLYD 546
               SCOP domains d1xg2a_ A: automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1xg2A00 A:1-317 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---Pectinesterase-1xg2A01 A:4-301                                                                                                                                                                                                                                                                            ---------------- Pfam domains
         Sec.struct. author ....eee.........hhhhhhhhh.......eeeee..eeee..eee......eeeee.....eeeee.........hhhhh.eee.....eee..eeee..hhhhh....eee....eeee..eee.....eee...eeeee..eeee....eee..eeeee..eeee........eeeeee.........eeeee..eeee...hhhhh....eeee.......eeeee..ee.....................eeeee.................eeee.hhhhhh..hhhhhh.hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------PECTINESTERASE_1    ---------------------------------------------------------------------------------------------------PECTINESTE---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg2 A   1 IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVAYVDGLYD 317
                                    10        20        30        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       300       310       

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with PMEI_ACTDE | P83326 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:151
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
           PMEI_ACTDE    32 AENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTNQATDPKLKGRYETCSENYADAIDSLGQAKQFLTSGDYNSLNIYASAAFDGAGTCEDSFEGPPNIPTQLHQADLKLEDLCDIVLVISNLLP 182
               SCOP domains d1xg2b_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -PMEI-1xg2B01 B:1-145                                                                                                                             ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg2 B   0 FENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTNQATDPKLKGRYETCSENYADAIDSLGQAKQFLTSGDYNSLNIYASAAFDGAGTCEDSFEGPPNIPTQLHQADLKLEDLCDIVLVISNLLP 150
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PME1_SOLLC | P14280)
molecular function
    GO:0045330    aspartyl esterase activity    Catalysis of the hydrolysis of an ester bond by a mechanism involving a catalytically active aspartic acid residue.
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    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:0030599    pectinesterase activity    Catalysis of the reaction: pectin + n H2O = n methanol + pectate.
    GO:0046910    pectinesterase inhibitor activity    Stops, prevents or reduces the activity of any pectinesterase enzyme.
biological process
    GO:0042545    cell wall modification    The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.
    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:0009835    fruit ripening    An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0045490    pectin catabolic process    The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.
cellular component
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    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.

Chain B   (PMEI_ACTDE | P83326)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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