1YNU - JenaLib

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Title :   CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH L-VINYLGLYCINE

Authors :   G. Capitani, M. Tschopp, A. C. Eliot, J. F. Kirsch, M. G. Grutter

Date :   25 Jan 05 (Deposition) - 03 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Capitani, M. Tschopp, A. C. Eliot, J. F. Kirsch, M. G. Grutter
Structure Of Acc Synthase Inactivated By The Mechanism-Base Inhibitor L-Vinylglycine.
Febs Lett. V. 579 2458 2005
PubMed-ID: 15848188 | Reference-DOI: 10.1016/J.FEBSLET.2005.03.048

Molecule 1 - 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE
	Chains	:	A
	EC Number	:	4.4.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET19BV435STOPACS
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ACS-1
	Organism Scientific	:	MALUS X DOMESTICA
	Organism Taxid	:	3750
	Strain	:	GOLDEN DELICIOUS
	Synonym	:	ACC SYNTHASE, S-ADENOSYL-L-METHIONINE METHYLTHIOADENOSINE- LYASE
	Tissue	:	FRUIT CORTICAL TISSUE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION
2	NI	2	Ligand/Ion	NICKEL (II) ION
3	PY4	1	Ligand/Ion	2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PY4	2	Ligand/Ion	2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID
4	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PY4	1	Ligand/Ion	2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:113 , ASP A:290 , HOH A:928 , HOH A:983 , HOH A:1019	BINDING SITE FOR RESIDUE NI A 701
2	AC2	SOFTWARE	ASP A:84 , HIS A:86 , TRS A:901 , HOH A:1012	BINDING SITE FOR RESIDUE NI A 702
3	AC3	SOFTWARE	LEU A:304 , HOH A:927	BINDING SITE FOR RESIDUE K A 801
4	AC4	SOFTWARE	TYR A:19 , LEU A:45 , ALA A:46 , GLU A:47 , GLY A:119 , ALA A:120 , THR A:121 , TYR A:145 , ASN A:202 , ASP A:230 , ILE A:232 , TYR A:233 , SER A:270 , SER A:272 , LYS A:273 , ARG A:281 , ARG A:407 , HOH A:982	BINDING SITE FOR RESIDUE PY4 A 600
5	AC5	SOFTWARE	GLU A:27 , GLN A:83 , ASP A:84 , TYR A:85 , HIS A:86 , NI A:702	BINDING SITE FOR RESIDUE TRS A 901

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

Asymmetric Unit

No.	Residues
1	Thr A:142	-	Pro A:143
2	Asn A:199	-	Pro A:200
3	Asn A:202	-	Pro A:203
4	Ser A:240	-	Pro A:241

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_1	PS00105	Aminotransferases class-I pyridoxal-phosphate attachment site.	1A1C_MALDO	270-283	1	A:270-283

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_1	PS00105	Aminotransferases class-I pyridoxal-phosphate attachment site.	1A1C_MALDO	270-283	2	A:270-283

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_1	PS00105	Aminotransferases class-I pyridoxal-phosphate attachment site.	1A1C_MALDO	270-283	1	A:270-283

(no "Exon" information available for 1YNU)

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:417
 aligned with 1A1C_MALDO | P37821 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:430
                                    13        23        33        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       413       423       433
           1A1C_MALDO     4 LSRNATFNSHGQDSSYFLGWQEYEKNPYHEVHNTNGIIQMGLAENQLCFDLLESWLAKNPEAAAFKKNGESIFAELALFQDYHGLPAFKKAMVDFMAEIRGNKVTFDPNHLVLTAGATSANETFIFCLADPGEAVLIPTPYYPGFDRDLKWRTGVEIVPIHCTSSNGFQITETALEEAYQEAEKRNLRVKGVLVTNPSNPLGTTMTRNELYLLLSFVEDKGIHLISDEIYSGTAFSSPSFISVMEVLKDRNCDENSEVWQRVHVVYSLSKDLGLPGFRVGAIYSNDDMVVAAATKMSSFGLVSSQTQHLLSAMLSDKKLTKNYIAENHKRLKQRQKKLVSGLQKSGISCLNGNAGLFCWVDMRHLLRSNTFEAEMELWKKIVYEVHLNISPGSSCHCTEPGWFRVCFANLPERTLDLAMQRLKAFVGEYY 433
               SCOP domains d1ynua       _ A: 1-aminocyclopropane-1-carboxylate synthase (ACC synthase)                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1ynuA0       1 A:4-62,A:308-433                            1ynuA02 A:63-307 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                 1ynuA01 A:4-62,A:308-433 Aspartate Aminotransferase, domain 1                                                                  CATH domains
               Pfam domains ------       -----------------------Aminotran_1_2-1ynuA01 A:40-425                                                                                                                                                                                                                                                                                                                                                                    -------- Pfam domains
         Sec.struct. author ......-------hhhhhhhhhhhhh...........ee........hhhhhhhhhhhh.hhhh.ee..eehhhhhhhh.....hhhhhhhhhhhhhhhh......hhh.eeeeehhhhhhhhhhhhhh....eeeee.....hhhhhh......eeeee..hhhhh...hhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh.......hhhhhh..------.hhhh.eeeeee......hhhh.eeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh...hhhhhhhhhhhhhhh..ee.ee..........eeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ynu A   4 LSRNAT-------SSYFLGWQEYEKNPYHEVHNTNGIIQMGLAENQLCFDLLESWLAKNPEAAAFKKNGESIFAELALFQDYHGLPAFKKAMVDFMAEIRGNKVTFDPNHLVLTAGATSANETFIFCLADPGEAVLIPTPYYPGFDRDLKWRTGVEIVPIHCTSSNGFQITETALEEAYQEAEKRNLRVKGVLVTNPSNPLGTTMTRNELYLLLSFVEDKGIHLISDEIYSGTAFSSPSFISVMEVLKD------SEVWQRVHVVYSLSKDLGLPGFRVGAIYSNDDMVVAAATKMSSFGLVSSQTQHLLSAMLSDKKLTKNYIAENHKRLKQRQKKLVSGLQKSGISCLNGNAGLFCWVDMRHLLRSNTFEAEMELWKKIVYEVHLNISPGSSCHCTEPGWFRVCFANLPERTLDLAMQRLKAFVGEYY 433
                                 |   -   |    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        |-     | 263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
                                 9      17                                                                                                                                                                                                                                        252    259

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: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: GABA-aminotransferase-like (167)

Protein domain: 1-aminocyclopropane-1-carboxylate synthase (ACC synthase) (7)

Apple (Malus domestica) [TaxId: 3750] (5)

d1ynua_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Aminotran_1_2 (77)

Malus domestica (Apple) (Pyrus malus) (3)

Aminotran_1_2-1ynuA01

A:40-425

Asymmetric Unit(hide GO term definitions)

Chain A (1A1C_MALDO | P37821)

molecular function
	GO:0016847	1-aminocyclopropane-1-carboxylate synthase activity	Catalysis of the reaction: S-adenosyl-L-methionine(1+) = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine + H(+).
	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: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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0042218	1-aminocyclopropane-1-carboxylate biosynthetic process	The chemical reactions and pathways resulting in the formation of 1-aminocyclopropane-1-carboxylate, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0009693	ethylene biosynthetic process	The chemical reactions and pathways resulting in the formation of ethylene (C2-H4, ethene), a simple hydrocarbon gas that can function in plants as a growth regulator.
	GO:0009835	fruit ripening	An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asn A:199 - Pro A:200	[ RasMol ]
		Asn A:202 - Pro A:203	[ RasMol ]
		Ser A:240 - Pro A:241	[ RasMol ]
		Thr A:142 - Pro A:143	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1ynu
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	4.4.1.14
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	1A1C_MALDO \| P37821	:	1b8g 1m4n 1m7y 3piu

1b8g	THE NATIVE STRUCTURE OF APPLE ACC SYNTHASE
1m4n	THE STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH AN AMINO-OXY ANALOGUE OF THE SUBSTRATE
1m7y	THE STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH THE INHIBITOR L-AMINOETHOXYVINYLGLYCINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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Gene Ontology (9, 9)

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