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Description

Title :   CRYSTAL STRUCTURE OF PEACH PRU P3, THE PROTOTYPIC MEMBER OF THE FAMILY OF PLANT NON-SPECIFIC LIPID TRANSFER PROTEIN PAN-ALLERGENS

Authors :   N. Pasquato, R. Berni, C. Folli, S. Folloni, M. Cianci, S. Pantano, J. Helliwell, G. Zanotti

Date :   05 Aug 05 (Deposition) - 29 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (2x),B (2x)
Biol. Unit 4: A (2x),B (2x)
Biol. Unit 5: A (1x),B (1x)
Biol. Unit 6: B  (2x)

Keywords :   Non-Specific Lipid Transfer Protein, Ltp, Ns-Ltp, Food Allergen, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Pasquato, R. Berni, C. Folli, S. Folloni, M. Cianci, S. Pantano, J. R. Helliwell, G. Zanotti
Crystal Structure Of Peach Pru P 3, The Prototypic Member Of The Family Of Plant Non-Specific Lipid Transfer Protein Pan-Allergens
J. Mol. Biol. V. 356 684 2006
PubMed-ID: 16388823 | Reference-DOI: 10.1016/J.JMB.2005.11.063
(for further references see the PDB file header)

Compounds

Molecule 1 - NON-SPECIFIC LIPID TRANSFER PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11B
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LTP
	Organism Common	:	PEACH
	Organism Scientific	:	PRUNUS PERSICA
	Organism Taxid	:	3760

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A (2x)	B (2x)
Biological Unit 4 (2x)	:	A (2x)	B (2x)
Biological Unit 5 (1x)	:	A (1x)	B (1x)
Biological Unit 6 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 5)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	DAO	2	Ligand/Ion	LAURIC ACID
2	HP6	1	Ligand/Ion	HEPTANE
3	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DAO	1	Ligand/Ion	LAURIC ACID
2	HP6	1	Ligand/Ion	HEPTANE
3	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	DAO	1	Ligand/Ion	LAURIC ACID
2	HP6	-1	Ligand/Ion	HEPTANE
3	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	DAO	2	Ligand/Ion	LAURIC ACID
2	HP6	-1	Ligand/Ion	HEPTANE
3	P6G	2	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 6)

No.	Name	Count	Type	Full Name
1	DAO	2	Ligand/Ion	LAURIC ACID
2	HP6	-1	Ligand/Ion	HEPTANE
3	P6G	2	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 5 (3, 3)

No.	Name	Count	Type	Full Name
1	DAO	1	Ligand/Ion	LAURIC ACID
2	HP6	-1	Ligand/Ion	HEPTANE
3	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 6 (3, 6)

No.	Name	Count	Type	Full Name
1	DAO	2	Ligand/Ion	LAURIC ACID
2	HP6	-1	Ligand/Ion	HEPTANE
3	P6G	2	Ligand/Ion	HEXAETHYLENE GLYCOL
4	SO4	2	Ligand/Ion	SULFATE ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:26 , ASN A:29 , HOH A:209 , HOH A:255 , THR B:2 , GLY B:4	BINDING SITE FOR RESIDUE SO4 B 205
2	AC2	SOFTWARE	ARG A:44 , ALA A:47 , CYS A:48 , SER A:55 , LYS A:80 , ILE A:81 , SER A:82 , HP6 A:204	BINDING SITE FOR RESIDUE DAO A 202
3	AC3	SOFTWARE	ILE A:31 , LEU A:69 , DAO A:202	BINDING SITE FOR RESIDUE HP6 A 204
4	AC4	SOFTWARE	SER A:8 , SER B:7 , SER B:8 , VAL B:17 , ARG B:18 , ILE B:81	BINDING SITE FOR RESIDUE DAO B 201
5	AC5	SOFTWARE	ASN A:29 , ARG A:32 , ASN A:36 , VAL A:75 , MET B:0 , GLN B:5	BINDING SITE FOR RESIDUE P6G B 203

SS Bonds (8, 8)

Asymmetric Unit

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	2	A:69-90 B:69-90

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	1	A:69-90 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	1	- B:69-90

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	4	A:69-90 B:69-90

Biological Unit 4 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	4	A:69-90 B:69-90

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	2	A:69-90 B:69-90

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLANT_LTP	PS00597	Plant lipid transfer proteins signature.	NLTP1_PRUPE	69-90	2	- B:69-90

Exons (0, 0)

(no "Exon" information available for 2ALG)

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:92
 aligned with NLTP1_PRUPE | P81402 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:92
                             1                                                                                          
                             |       9        19        29        39        49        59        69        79        89  
           NLTP1_PRUPE    - -ITCGQVSSALAPCIPYVRGGGAVPPACCNGIRNVNNLARTTPDRQAACNCLKQLSASVPGVNPNNAAALPGKCGVHIPYKISASTNCATVK 91
               SCOP domains d2alga_ A: automated matches                                                                 SCOP domains
               CATH domains 2algA00 A:0-91 Plant lipid-transfer and hydrophobic proteins                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh............hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PLANT_LTP  PDB: A:69-9- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  2alg A  0 MITCGQVSSSLAPCIPYVRGGGAVPPACCNGIRNVNNLARTTPDRQAACNCLKQLSASVPGVNPNNAAALPGKCGVSIPYKISASTNCATVK 91
                                     9        19        29        39        49        59        69        79        89

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with NLTP1_PRUPE | P81402 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:92
                             1                                                                                          
                             |       9        19        29        39        49        59        69        79        89  
           NLTP1_PRUPE    - -ITCGQVSSALAPCIPYVRGGGAVPPACCNGIRNVNNLARTTPDRQAACNCLKQLSASVPGVNPNNAAALPGKCGVHIPYKISASTNCATVK 91
               SCOP domains d2algb_ B: automated matches                                                                 SCOP domains
               CATH domains 2algB00 B:0-91 Plant lipid-transfer and hydrophobic proteins                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...........hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PLANT_LTP  PDB: B:69-9- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  2alg B  0 MITCGQVSSSLAPCIPYVRGGGAVPPACCNGIRNVNNLARTTPDRQAACNCLKQLSASVPGVNPNNAAALPGKCGVSIPYKISASTNCATVK 91
                                     9        19        29        39        49        59        69        79        89

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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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin (42)

Superfamily: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin (42)

Family: Plant lipid-transfer and hydrophobic proteins (31)

Protein domain: automated matches (3)

Prunus persica [TaxId: 3760] (2)

1a	d2alga_	A:
1b	d2algb_	B:

CATH Domains (1, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Hydrophobic Seed Protein (33)

Homologous Superfamily: Plant lipid-transfer and hydrophobic proteins (33)

Peach (Prunus persica) (2)

1a	2algA00	A:0-91
1b	2algB00	B:0-91

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2ALG)

Gene Ontology (3, 3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NLTP1_PRUPE | P81402)

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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	2alg
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	NLTP1_PRUPE \| P81402	:	2b5s

Related Entries Specified in the PDB File

1bwo	THE CRYSTAL STRUCTURE OF WHEAT NON-SPECIFIC TRANSFER PROTEIN COMPLEXED WITH TWO MOLECULES OF PHOSPHOLIPID AT 2.1 A RESOLUTION
1fk0	STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH CAPRIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY
1mid	NON-SPECIFIC LIPID TRANSFER PROTEIN 1 FROM BARLEY IN COMPLEX WITH L-ALFA-LYSOPHOSPHATIDYLCHOLINE, LAUDOYL
1mzl	MAIZE NONSPECIFIC LIPID TRANSFER PROTEIN
1rzl	RICE NONSPECIFIC LIPID TRANSFER PROTEIN