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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PGIP (POLYGALACTURONASE INHIBITING PROTEIN), A LEUCINE RICH REPEAT PROTEIN INVOLVED IN PLANT DEFENSE
 
Authors :  A. Di Matteo, L. Federici, B. Mattei, G. Salvi, K. A. Johnson, C. Savino, G. De Lorenzo, D. Tsernoglou, F. Cervone
Date :  08 May 03  (Deposition) - 24 Jul 03  (Release) - 25 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Polygalacturonase Inhibiting Protein, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Di Matteo, L. Federici, B. Mattei, G. Salvi, K. A. Johnson, C. Savino, G. De Lorenzo, D. Tsernoglou, F. Cervone
The Crystal Structure Of Polygalacturonase- Inhibiting Protein (Pgip), A Leucine-Rich Repeat Protein Involved In Plant Defense
Proc. Natl. Acad. Sci. Usa V. 100 10124 2003
PubMed-ID: 12904578  |  Reference-DOI: 10.1073/PNAS.1733690100

(-) Compounds

Molecule 1 - POLYGALACTURONASE INHIBITING PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemNICOTIANA BENTHAMIANA
    Expression System Taxid4100
    Expression System VectorPVX
    Organism CommonKIDNEY BEAN
    Organism ScientificPHASEOLUS VULGARIS
    Organism Taxid3885
    SynonymPGIP-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:2 , ASP A:32 , ASN A:35 , ARG A:36 , SER A:219BINDING SITE FOR RESIDUE NAG A1314
2AC2SOFTWAREASN A:87 , HIS A:110 , THR A:111 , ASN A:112 , TYR A:134 , NAG A:1316 , HOH A:2135 , HOH A:2311 , HOH A:2313BINDING SITE FOR RESIDUE NAG A1315
3AC3SOFTWARENAG A:1315 , HOH A:2282BINDING SITE FOR RESIDUE NAG A1316
4AC4SOFTWAREARG A:252 , ASN A:274 , SER A:276 , SER A:296 , HOH A:2234 , HOH A:2315 , HOH A:2316BINDING SITE FOR RESIDUE NAG A1317
5AC5SOFTWAREGLY A:59 , LEU A:60 , ASN A:61 , GLY A:85 , ILE A:86 , ASN A:87 , HOH A:2318 , HOH A:2319 , HOH A:2320BINDING SITE FOR RESIDUE ACT A1318

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:33
2A:34 -A:43
3A:281 -A:303
4A:305 -A:312

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OGQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OGQ)

(-) 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:313
 aligned with PGIP2_PHAVU | P58822 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:313
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339   
          PGIP2_PHAVU    30 ELCNPQDKQALLQIKKDLGNPTTLSSWLPTTDCCNRTWLGVLCDTDTQTYRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQGGNLQRFDVSAYANNKCLCGSPLPACT 342
               SCOP domains d1ogqa_ A: Polygalacturonase inhibiting protein PGIP                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ogqA00 A:1-313 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) ---LRRNT_2-1ogqA03 A:4-44                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_1-1ogqA01 A:269-293  -------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_1-1ogqA02 A:269-293  -------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhh...............eee........eeeeeee.......ee.hhhhhhh....eeeeeee..ee...hhhhhhh....eeeeeee..eee.hhhhhhh....eee....eee...hhhhhhh....eee......eee.hhhhhh......eee....eeeee.hhhhhhh...eee....eeee.hhhhh.......eee....ee...hhhh.......eee......ee..hhhhhhh....eee....eeeee.....hhhhhhhhhh....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogq A   1 ELCNPQDKQALLQIKKDLGNPTTLSSWLPTTDCCNRTWLGVLCDTDTQTYRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQGGNLQRFDVSAYANNKCLCGSPLPACT 313
                                    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   

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: LRR (77)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGIP2_PHAVU | P58822)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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