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Title :   CRYSTAL STRUCTURE OF THE RIBOSOME INACTIVATING PROTEIN PDL1

Authors :   A. Ruggiero, A. Di Maro, V. Severino, A. Chambery, R. Berisio

Date :   22 Apr 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Protein, Ribosome Inactivation, Disulfide Bond, Glycoprotein, Hydrolase, Plant Defense, Protein Synthesis Inhibitor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ruggiero, A. Di Maro, V. Severino, A. Chambery, R. Berisio
Crystal Structure Of Pd-L1, A Ribosome Inactivating Protein From Phytolacca Dioica L. Leaves With The Property To Induc Dna Cleavage
Biopolymers V. 91 1135 2009
PubMed-ID: 19452522 | Reference-DOI: 10.1002/BIP.21260

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN PD-L1/PD-L2
	Chains	:	A, B
	EC Number	:	3.2.2.22
	Organism Common	:	BELLA SOMBRA TREE
	Organism Scientific	:	PHYTOLACCA DIOICA
	Organism Taxid	:	29725
	Synonym	:	RRNA N-GLYCOSIDASE PD-L1/PD-L2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , HOH A:630 , HOH A:634 , HOH A:673 , HOH A:741 , HOH A:815	BINDING SITE FOR RESIDUE NAG A 263
2	AC2	SOFTWARE	SER A:120 , TYR A:122 , ILE A:170 , HOH A:378 , HOH A:412 , HOH A:507	BINDING SITE FOR RESIDUE EDO A 264
3	AC3	SOFTWARE	ASN B:10 , HOH B:643 , HOH B:804	BINDING SITE FOR RESIDUE NAG B 262
4	AC4	SOFTWARE	SER B:120 , TYR B:122 , ILE B:170 , HOH B:439 , HOH B:448	BINDING SITE FOR RESIDUE EDO B 265

Asymmetric Unit

No.	Residues
1	A:34	-	A:258
2	A:84	-	A:105
3	B:34	-	B:258
4	B:84	-	B:105

(no "Cis Peptide Bond" information available for 3H5K)

(no "SAP(SNP)/Variant" information available for 3H5K)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIPL1_PHYDI	170-186	2	A:170-186 B:170-186

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIPL1_PHYDI	170-186	1	A:170-186 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIPL1_PHYDI	170-186	1	- B:170-186

(no "Exon" information available for 3H5K)

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:261
 aligned with RIPL1_PHYDI | P84853 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
          RIPL1_PHYDI     1 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 261
               SCOP domains d3h5ka_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3h5kA01 A:1-177 Ricin (A subunit), domain 1                                                                                                                                      3h5kA02 A:178-258 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.hhh.eeeeeee.....eeeeeeee..eeeeee.....hhhhhhhhhhhh.....eee.......hhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeehhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h5k A   1 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 261
                                    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

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with RIPL1_PHYDI | P84853 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    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 
          RIPL1_PHYDI     1 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 261
               SCOP domains d3h5kb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3h5kB01 B:1-177 Ricin (A subunit), domain 1                                                                                                                                      3h5kB02 B:178-258 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.hhh.eeeeeee.....eeeeeeee..eeeeee....hhhhhhhhhhhhh.....eee.......hhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeehhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h5k B   1 INTITYDAGNTTINKYATFMESLRNEAKDPSLQCYGIPMLPNNSSTIKYLLVKLQGASQKTITLMLRRNNLYVMGYSDPFNGNCRYHIFNDITGTERTNVENTLCSSSSSRDAKPINYNSLYSTLEKKAEVNSRSQVQLGIQILSSDIGKISGQSSFTDKTEAKFLLVAIQMVSEAARFKYIENQVKTNFNRDFSPNDKILDLEENWGKISTAIHDATNGALPKPLELKNADGTKWIVLRVDEIKPDMGLLNYVNGTCQTT 261
                                    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

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ribosome inactivating proteins (RIP) (180)

Superfamily: Ribosome inactivating proteins (RIP) (180)

Family: Plant cytotoxins (166)

Protein domain: automated matches (73)

Phytolacca dioica [TaxId: 29725] (6)

1a	d3h5ka_	A:
1b	d3h5kb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Ricin (A subunit); domain 1 (112)

Homologous Superfamily: Ricin (A subunit), domain 1 (112)

Bella sombra tree (Phytolacca dioica) (2)

1a	3h5kA01	A:1-177
1b	3h5kB01	B:1-177

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Ricin (A Subunit), domain 2 (112)

Homologous Superfamily: Ricin (A Subunit), domain 2 (112)

Bella sombra tree (Phytolacca dioica) (2)

2a	3h5kA02	A:178-258
2b	3h5kB02	B:178-258

(no "Pfam Domain" information available for 3H5K)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIPL1_PHYDI | P84853)

molecular function
	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:0030598	rRNA N-glycosylase activity	Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
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.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Asymmetric Unit
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Biological Units
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	RIPL1_PHYDI \| P84853	:	3le7

2qet	STRUCTURE OF THE MUTANT S211A OF THE RIBOSOME INACTIVATING PROTEIN PDL4 FROM P. DIOICA IN COMPLEX WITH ADENINE
2z4u	CRYSTAL STRUCTURE OF WILD TYPE PD-L4 FROM PHYTOLACCA DIOICA LEAVES
2z53	CRYSTAL STRUCTURE OF THE S211A MUTANT OF THE RIBOSOME INACTIVATING PROTEIN PDL4 FROM P. DIOICA LEAVES

Description

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