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(-) Description

Title :  THE STRUCTURE OF PHASEOLIN AT 2.2 ANGSTROMS RESOLUTION: IMPLICATIONS FOR A COMMON VICILIN(SLASH)LEGUMIN STRUCTURE AND THE GENETIC ENGINEERING OF SEED STORAGE PROTEINS
 
Authors :  M. C. Lawrence, T. Izard, M. Beuchat, R. J. Blagrove, P. M. Colman
Date :  07 Jul 94  (Deposition) - 30 Sep 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Plant Seed Storage Protein(Vicilin) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Lawrence, T. Izard, M. Beuchat, R. J. Blagrove, P. M. Colman
Structure Of Phaseolin At 2. 2 A Resolution. Implications Fo A Common Vicilin/Legumin Structure And The Genetic Engineering Of Seed Storage Proteins.
J. Mol. Biol. V. 238 748 1994
PubMed-ID: 8182747  |  Reference-DOI: 10.1006/JMBI.1994.1333
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHASEOLIN
    Chains: A, B, C
    Engineered: YES
    Organism Scientific: PHASEOLUS VULGARIS
    Organism Taxid: 3885

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:224 , GLU A:225 , PHE A:226 , GLY A:227 , ASN A:228 , GLU A:245 , GLU A:247BINDING SITE FOR RESIDUE NAG A 900
2AC2SOFTWAREASN B:224 , GLU B:225 , ASN B:228BINDING SITE FOR RESIDUE NAG B 901
3AC3SOFTWAREASN C:224 , GLU C:225 , PHE C:226 , ASN C:228 , GLU C:247BINDING SITE FOR RESIDUE NAG C 902
4AC4SOFTWAREHIS A:32 , ARG A:34 , GLU A:56 , ARG A:58 , ARG A:130 , LYS A:296 , ASP A:297BINDING SITE FOR RESIDUE PO4 A 950
5AC5SOFTWAREHIS B:32 , GLU B:56 , ARG B:58 , ARG B:130 , LYS B:296 , ASP B:297BINDING SITE FOR RESIDUE PO4 B 951
6AC6SOFTWAREHIS C:32 , ARG C:34 , GLU C:56 , ARG C:58 , ARG C:79 , ARG C:130 , LYS C:296 , ASP C:297BINDING SITE FOR RESIDUE PO4 C 952

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PHL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PHL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PHL)

(-) 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:360
 aligned with PHSB_PHAVU | P02853 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:371
                                    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 
           PHSB_PHAVU    35 DNPFYFNSDNSWNTLFKNQYGHIRVLQRFDQQSKRLQNLEDYRLVEFRSKPETLLLPQQADAELLLVVRSGSAILVLVKPDDRREYFFLTSDNPIFSDHQKIPAGTIFYLVNPDPKEDLRIIQLAMPVNNPQIHEFFLSSTEAQQSYLQEFSKHILEASFNSKFEEINRVLFEEEGQQEGVIVNIDSEQIKELSKHAKSSSRKSLSKQDNTIGNEFGNLTERTDNSLNVLISSIEMEEGALFVPHYYSKAIVILVVNEGEAHVELVGPKGNKETLEYESYRAELSKDDVFVIPAAYPVAIKATSNVNFTGFGINANNNNRNLLAGKTDNVISSIGRALDGKDVLGLTFSGSGDEVMKLINKQSGSYFVDAH 405
               SCOP domains d2phla1 A:11-210 Seed storage 7S protein                                                                                                                                                                         d2phla2 A:220-381 Seed storage 7S protein                                                                                                                          SCOP domains
               CATH domains ------2phlA01 A:17-220 Jelly Rolls                                                                                                                                                                                2phlA02 A:221-381 Jelly Rolls                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeeeeeee.eeeeeeee...............eeeeeeee.eeeeeeeeee.eeeeeeeeeeeeeeeee...eeeeeeeee......eeeee....eeeeee......eeeeeeee.......eeeee.......hhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeee....hhhhhhhhhh.---------eeeee.eeeeeeeee...eeeeeeeeee.eeeeeeeeee..eeeeeeee...eeeeee...--.....eeeee.....eeeee....eeeeee...eeeeeeeee....eeeee......hhhhhhh..hhhhhhhhhh..hhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phl A  11 DNPFYFNSDNSWNTLFKNQYGHIRVLQRFDQQSKRLQNLEDYRLVEFRSKPETLLLPQQADAELLLVVRSGSAILVLVKPDDRREYFFLTSDNPIFSDHQKIPAGTIFYLVNPDPKEDLRIIQLAMPVNNPQIHEFFLSSTEAQQSYLQEFSKHILEASFNSKFEEINRVLFEEEGQQEGVIVNIDSEQIKELSKHAKSS---------NTIGNEFGNLTERTDNSLNVLISSIEMEEGALFVPHYYSKAIVILVVNEGEAHVELVGPKG--ETLEYESYRAELSKDDVFVIPAAYPVAIKATSNVNFTGFGINANNNNRNLLAGKTDNVISSIGRALDGKDVLGLTFSGSGDEVMKLINKQSGSYFVDAH 381
                                    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       320       330       340       350       360       370       380 
                                                                                                                                                                                                                                 210       220                                                         280  |                                                                                                  
                                                                                                                                                                                                                                                                                                          283                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:360
 aligned with PHSB_PHAVU | P02853 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:371
                                    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 
           PHSB_PHAVU    35 DNPFYFNSDNSWNTLFKNQYGHIRVLQRFDQQSKRLQNLEDYRLVEFRSKPETLLLPQQADAELLLVVRSGSAILVLVKPDDRREYFFLTSDNPIFSDHQKIPAGTIFYLVNPDPKEDLRIIQLAMPVNNPQIHEFFLSSTEAQQSYLQEFSKHILEASFNSKFEEINRVLFEEEGQQEGVIVNIDSEQIKELSKHAKSSSRKSLSKQDNTIGNEFGNLTERTDNSLNVLISSIEMEEGALFVPHYYSKAIVILVVNEGEAHVELVGPKGNKETLEYESYRAELSKDDVFVIPAAYPVAIKATSNVNFTGFGINANNNNRNLLAGKTDNVISSIGRALDGKDVLGLTFSGSGDEVMKLINKQSGSYFVDAH 405
               SCOP domains d2phlb1 B:11-210 Seed storage 7S protein                                                                                                                                                                         d2phlb2 B:220-381 Seed storage 7S protein                                                                                                                          SCOP domains
               CATH domains ------2phlB01 B:17-220 Jelly Rolls                                                                                                                                                                                2phlB02 B:221-379 Jelly Rolls                                                                                                                                  -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeeeeeee.eeeeeeee...............eeeeeeee.eeeeeeeeee.eeeeeeeeeeeeeeeee...eeeeeeeee......eeeee....eeeeee......eeeeeeee.......eeeee.......hhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeee....hhhhhhhhhh.---------eeeee.eeeeeeeee...eeeeeeeeee.eeeeeeeeee..eeeeeeee...eeeeee...--.....eeeee.....eeeee....eeeeee...eeeeeeeee....eeeee......hhhhhhh..hhhhhhhhhh..hhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phl B  11 DNPFYFNSDNSWNTLFKNQYGHIRVLQRFDQQSKRLQNLEDYRLVEFRSKPETLLLPQQADAELLLVVRSGSAILVLVKPDDRREYFFLTSDNPIFSDHQKIPAGTIFYLVNPDPKEDLRIIQLAMPVNNPQIHEFFLSSTEAQQSYLQEFSKHILEASFNSKFEEINRVLFEEEGQQEGVIVNIDSEQIKELSKHAKSS---------NTIGNEFGNLTERTDNSLNVLISSIEMEEGALFVPHYYSKAIVILVVNEGEAHVELVGPKG--ETLEYESYRAELSKDDVFVIPAAYPVAIKATSNVNFTGFGINANNNNRNLLAGKTDNVISSIGRALDGKDVLGLTFSGSGDEVMKLINKQSGSYFVDAH 381
                                    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       320       330       340       350       360       370       380 
                                                                                                                                                                                                                                 210       220                                                         280  |                                                                                                  
                                                                                                                                                                                                                                                                                                          283                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:361
 aligned with PHSB_PHAVU | P02853 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:372
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403  
           PHSB_PHAVU    34 QDNPFYFNSDNSWNTLFKNQYGHIRVLQRFDQQSKRLQNLEDYRLVEFRSKPETLLLPQQADAELLLVVRSGSAILVLVKPDDRREYFFLTSDNPIFSDHQKIPAGTIFYLVNPDPKEDLRIIQLAMPVNNPQIHEFFLSSTEAQQSYLQEFSKHILEASFNSKFEEINRVLFEEEGQQEGVIVNIDSEQIKELSKHAKSSSRKSLSKQDNTIGNEFGNLTERTDNSLNVLISSIEMEEGALFVPHYYSKAIVILVVNEGEAHVELVGPKGNKETLEYESYRAELSKDDVFVIPAAYPVAIKATSNVNFTGFGINANNNNRNLLAGKTDNVISSIGRALDGKDVLGLTFSGSGDEVMKLINKQSGSYFVDAH 405
               SCOP domains d2phlc1 C:10-210 Seed storage 7S protein                                                                                                                                                                          d2phlc2 C:220-381 Seed storage 7S protein                                                                                                                          SCOP domains
               CATH domains -------2phlC01 C:17-220 Jelly Rolls                                                                                                                                                                                2phlC02 C:221-379 Jelly Rolls                                                                                                                                  -- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------         Cupin_1-2phlC01 C:220-366                                                                                                                          --------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------         Cupin_1-2phlC02 C:220-366                                                                                                                          --------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------         Cupin_1-2phlC03 C:220-366                                                                                                                          --------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------         Cupin_1-2phlC04 C:220-366                                                                                                                          --------------- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------         Cupin_1-2phlC05 C:220-366                                                                                                                          --------------- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------         Cupin_1-2phlC06 C:220-366                                                                                                                          --------------- Pfam domains (6)
         Sec.struct. author ....eee....eeeeeeee.eeeeeeee...............eeeeeeee.eeeeeeeeee.eeeeeeeeeeeeeeeee...eeeeeeeee......eeeee....eeeeee......eeeeeeee.......eeeee.......hhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeee....hhhhhhhhhh.---------eeeee.eeeeeeeee...eeeeeeeeee.eeeeeeeeee..eeeeeeee...eeeeee...--.....eeeee.....eeeee....eeeeee...eeeeeeeee....eeeee......hhhhhhh..hhhhhhhhhh..hhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2phl C  10 QDNPFYFNSDNSWNTLFKNQYGHIRVLQRFDQQSKRLQNLEDYRLVEFRSKPETLLLPQQADAELLLVVRSGSAILVLVKPDDRREYFFLTSDNPIFSDHQKIPAGTIFYLVNPDPKEDLRIIQLAMPVNNPQIHEFFLSSTEAQQSYLQEFSKHILEASFNSKFEEINRVLFEEEGQQEGVIVNIDSEQIKELSKHAKSS---------NTIGNEFGNLTERTDNSLNVLISSIEMEEGALFVPHYYSKAIVILVVNEGEAHVELVGPKG--ETLEYESYRAELSKDDVFVIPAAYPVAIKATSNVNFTGFGINANNNNRNLLAGKTDNVISSIGRALDGKDVLGLTFSGSGDEVMKLINKQSGSYFVDAH 381
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209|        -|      229       239       249       259       269       279|  |   289       299       309       319       329       339       349       359       369       379  
                                                                                                                                                                                                                                  210       220                                                         280  |                                                                                                  
                                                                                                                                                                                                                                                                                                           283
   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, 6)

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

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: Jelly Rolls (177)
(-)
Phaseolus vulgaris. Organism_taxid: 3885 (1)
1a2phlB02B:221-379
1b2phlC02C:221-379
1c2phlA02A:221-381
1d2phlA01A:17-220
1e2phlB01B:17-220
1f2phlC01C:17-220

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PHSB_PHAVU | P02853)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
cellular component
    GO:0033095    aleurone grain    A membrane-bounded storage granule found in cells of the aleurone layer in plants; contains either a protein matrix, protein-carbohydrate bodies and/or globoids. Aleurone grains are formed by the vacuole, rough endoplasmic reticulum and dictyosomes.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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

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        PHSB_PHAVU | P02853: 1phs

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