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Title :   PETAL DEATH PROTEIN PSR132 WITH CYSTEINE-LINKED GLUTARALDEHYDE FORMING A THIOHEMIACETAL ADDUCT

Authors :   A. Teplyakov, S. Liu, Z. Lu, A. Howard, D. Dunaway-Mariano, O. Herzberg

Date :   08 May 05 (Deposition) - 03 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Tim-Barrel, Helix Swapping, 2-Ethyl-3-Methylmalate Lyase, 2-Propyl-3- Methylmalate Lyase, Lyase/Pep Mutase Superfamily, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Teplyakov, S. Liu, Z. Lu, A. Howard, D. Dunaway-Mariano, O. Herzber
Crystal Structure Of The Petal Death Protein From Carnation Flower.
Biochemistry V. 44 16377 2005
PubMed-ID: 16342930 | Reference-DOI: 10.1021/BI051779Y

Molecule 1 - PETAL DEATH PROTEIN
	Chains	:	A, B
	EC Number	:	4.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSR132-PET3A
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PSR132
	Organism Common	:	CLOVE PINK
	Organism Scientific	:	DIANTHUS CARYOPHYLLUS
	Organism Taxid	:	3570
	Synonym	:	PSR132

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GAQ	2	Ligand/Ion	5-HYDROXYPENTANAL
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	GAQ	4	Ligand/Ion	5-HYDROXYPENTANAL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:79 , ASP A:107 , ASP A:109 , LYS A:142 , GAQ A:402	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	ASP B:79 , ASP B:107 , LYS B:142 , GAQ B:402	BINDING SITE FOR RESIDUE MG B 401
3	AC3	SOFTWARE	CYS A:144 , GLY A:145 , ARG A:179 , ASN A:231 , ILE A:233 , LEU A:258 , MG A:401	BINDING SITE FOR RESIDUE GAQ A 402
4	AC4	SOFTWARE	TYR B:68 , CYS B:144 , GLY B:145 , ARG B:179 , GLU B:209 , ASN B:231 , ILE B:233 , LEU B:258 , MG B:401	BINDING SITE FOR RESIDUE GAQ B 402

(no "SS Bond" information available for 1ZLP)

Asymmetric Unit

No.	Residues
1	Trp A:140	-	Pro A:141
2	Trp B:140	-	Pro B:141

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISOCITRATE_LYASE	PS00161	Isocitrate lyase signature.	PDP_DIACA	142-147	2	A:142-147 B:142-147

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISOCITRATE_LYASE	PS00161	Isocitrate lyase signature.	PDP_DIACA	142-147	4	A:142-147 B:142-147

(no "Exon" information available for 1ZLP)

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
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Chain A from PDB  Type:PROTEIN  Length:284
 aligned with PDP_DIACA | Q05957 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:284
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    
            PDP_DIACA    28 KTTMHRLIEEHGSVLMPGVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVEATRRITAAAPNLCVVVDGDTGGGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGKAVVPAEEHALKIAAAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEAPANVDELKEVSAKTKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVNIMKILKEKGTTRDDLDQMATFSEFNELISLESWYEMESKFK 311
               SCOP domains d1zlpa_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeeehhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeeee.........hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ISOCIT-------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zlp A  28 KTTMHRLIEEHGSVLMPGVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVEATRRITAAAPNLCVVVDGDTGGGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGKAVVPAEEHALKIAAAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEAPANVDELKEVSAKTKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVNIMKILKEKGTTRDDLDQMATFSEFNELISLESWYEMESKFK 311
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with PDP_DIACA | Q05957 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:285
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     
            PDP_DIACA    28 KTTMHRLIEEHGSVLMPGVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVEATRRITAAAPNLCVVVDGDTGGGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGKAVVPAEEHALKIAAAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEAPANVDELKEVSAKTKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVNIMKILKEKGTTRDDLDQMATFSEFNELISLESWYEMESKFKN 312
               SCOP domains d1zlpb_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---PEP_mutase-1zlpB01 B:31-276                                                                                                                                                                                                                           ------------------------------------ Pfam domains (1)
           Pfam domains (2) ---PEP_mutase-1zlpB02 B:31-276                                                                                                                                                                                                                           ------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhh..eeeeee.hhhhhhhhhhh...eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhh...eeee..................hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeee..........hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zlp B  28 KTTMHRLIEEHGSVLMPGVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVEATRRITAAAPNLCVVVDGDTGGGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGKAVVPAEEHALKIAAAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEAPANVDELKEVSAKTKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVNIMKILKEKGTTRDDLDQMATFSEFNELISLESWYEMESKFKN 312
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307

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) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Phosphoenolpyruvate/pyruvate domain (92)

Family: automated matches (16)

Protein domain: automated matches (16)

Clove pink (Dianthus caryophyllus) [TaxId: 3570] (1)

1a	d1zlpa_	A:
1b	d1zlpb_	B:

(no "CATH Domain" information available for 1ZLP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PK_TIM (63)

Family: PEP_mutase (13)

Dianthus caryophyllus (Carnation) (Clove pink) (1)

1a	PEP_mutase-1zlpB01	B:31-276
1b	PEP_mutase-1zlpB02	B:31-276

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDP_DIACA | Q05957)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0047776	citramalate lyase activity	Catalysis of the reaction: S-citramalate = acetate + pyruvate.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030603	oxaloacetase activity	Catalysis of the reaction: H(2)O + oxaloacetate = acetate + H(+) + oxalate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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