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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF A POST TRANSLATIONAL MODIFIED BARLEY LTP1
 
Authors :  M. B. Lascombe, T. Prange, B. Bakan, D. Marion
Date :  27 Mar 09  (Deposition) - 15 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ltp1, Post-Transcriptional Modification, Oxylipin, Lipid- Binding, Lipoprotein, Transport, Lipid Binding Protein, Disulfide Bond, Lipid-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bakan, M. Hamberg, V. Larue, T. Prange, D. Marion, M. B. Lascombe
The Crystal Structure Of Oxylipin-Conjugated Barley Ltp1 Highlights The Unique Plasticity Of The Hydrophobic Cavity Of These Plant Lipid-Binding Proteins.
Biochem. Biophys. Res. Commun. V. 390 780 2009
PubMed-ID: 19836358  |  Reference-DOI: 10.1016/J.BBRC.2009.10.049

(-) Compounds

Molecule 1 - NON-SPECIFIC LIPID-TRANSFER PROTEIN 1
    Chains: A, B
    Organism Common: BARLEY
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: LTP 1, PROBABLE AMYLASE/PROTEASE INHIBITOR

 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  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ASY2Ligand/Ion(12E)-10-OXOOCTADEC-12-ENOIC ACID
2NA3Ligand/IonSODIUM ION
3TFA2Ligand/IonTRIFLUOROACETIC ACID
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ASY1Ligand/Ion(12E)-10-OXOOCTADEC-12-ENOIC ACID
2NA-1Ligand/IonSODIUM ION
3TFA1Ligand/IonTRIFLUOROACETIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ASY1Ligand/Ion(12E)-10-OXOOCTADEC-12-ENOIC ACID
2NA-1Ligand/IonSODIUM ION
3TFA1Ligand/IonTRIFLUOROACETIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:35 , HOH A:392 , ZN B:104 , ASY B:303 , HOH B:440 , HOH B:448BINDING SITE FOR RESIDUE ZN A 101
02AC2SOFTWAREASY A:302 , HOH A:376 , HOH A:397 , HIS B:35BINDING SITE FOR RESIDUE ZN A 102
03AC3SOFTWAREASN A:29 , ASP A:33 , HOH A:329 , HOH A:401BINDING SITE FOR RESIDUE ZN A 103
04AC4SOFTWARELEU A:63 , ALA A:67 , ILE A:81 , SER A:82 , HOH A:320BINDING SITE FOR RESIDUE NA A 201
05AC5SOFTWAREASP A:86 , ASP B:84 , HOH B:434BINDING SITE FOR RESIDUE NA A 203
06AC6SOFTWARELEU A:34 , HIS A:35 , ALA A:38 , VAL A:47 , VAL A:77 , PRO A:78 , TYR A:79 , HOH A:358 , HOH A:368BINDING SITE FOR RESIDUE TFA A 301
07AC7SOFTWAREASP A:7 , MET A:10 , GLY A:53 , ILE A:54 , ILE A:58 , ZN A:102 , HOH A:397 , HIS B:35 , ASN B:76 , HOH B:390BINDING SITE FOR RESIDUE ASY A 302
08AC8SOFTWAREASP A:84 , ZN A:101 , HOH A:392 , ARG B:56 , NA B:202 , HOH B:440BINDING SITE FOR RESIDUE ZN B 104
09AC9SOFTWAREASP A:84 , ARG B:56 , ZN B:104 , HOH B:440 , HOH B:441 , HOH B:448BINDING SITE FOR RESIDUE NA B 202
10BC1SOFTWARELEU B:34 , HIS B:35 , ALA B:38 , VAL B:47 , ASN B:76 , VAL B:77 , PRO B:78 , TYR B:79 , HOH B:373 , HOH B:388BINDING SITE FOR RESIDUE TFA B 302
11BC2SOFTWAREHIS A:35 , ASN A:76 , ZN A:101 , ASP B:7 , MET B:10 , LYS B:11 , GLY B:53 , ILE B:54 , ILE B:58 , ILE B:81 , HOH B:423 , HOH B:440 , HOH B:448BINDING SITE FOR RESIDUE ASY B 303

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:3 -A:50
2A:13 -A:27
3A:28 -A:73
4A:48 -A:87
5B:3 -B:50
6B:13 -B:27
7B:28 -B:73
8B:48 -B:87

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:22 -Pro A:23
2Gly B:22 -Pro B:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GSH)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PLANT_LTPPS00597 Plant lipid transfer proteins signature.NLTP1_HORVU95-116
 		  2A:69-90
B:69-90
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PLANT_LTPPS00597 Plant lipid transfer proteins signature.NLTP1_HORVU95-116
 		  1A:69-90
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PLANT_LTPPS00597 Plant lipid transfer proteins signature.NLTP1_HORVU95-116
 		  1-
B:69-90

(-) Exons   (0, 0)

(no "Exon" information available for 3GSH)

(-) 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:91
 aligned with NLTP1_HORVU | P07597 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:91
                                    36        46        56        66        76        86        96       106       116 
          NLTP1_HORVU    27 LNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTVCNCLKGIARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY 117
               SCOP domains d3gsha_ A: Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1)                      SCOP domains
               CATH domains 3gshA00 A:1-91 Plant lipid-transfer and hydrophobic proteins                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PLANT_LTP  PDB: A:69-9- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3gsh A   1 LNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTVCNCLKGIARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY  91
                                    10        20        30        40        50        60        70        80        90 


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with NLTP1_HORVU | P07597 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:91
                                    36        46        56        66        76        86        96       106       116 
          NLTP1_HORVU    27 LNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTVCNCLKGIARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY 117
               SCOP domains d3gshb_ B: Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1)                      SCOP domains
               CATH domains 3gshB00 B:1-91 Plant lipid-transfer and hydrophobic proteins                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PLANT_LTP  PDB: B:69-9- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3gsh B   1 LNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTVCNCLKGIARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY  91
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GSH)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NLTP1_HORVU | P07597)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NLTP1_HORVU | P07597: 1be2 1jtb 1lip 1mid

(-) Related Entries Specified in the PDB File

1mid THE ORIGINAL BARLEY LTP1 X-RAY STRUCTURE WITHOUT ANY COVALENT ADDUCT