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(-) Description

Title :  CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO-OXY)ETHYL](5'-DEOXYADENOSIN-5'-YL)(METHYL)SULFONIUM
 
Authors :  G. Capitani, A. C. Eliot, H. Gut, R. M. Khomutov, J. F. Kirsch, M. G. Grutt
Date :  03 Jul 02  (Deposition) - 22 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Fruit Ripening, Ethylene Biosynthesis, Pyridoxal Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Capitani, A. C. Eliot, H. Gut, R. M. Khomutov, J. F. Kirsch, M. G. Grutter
Structure Of 1-Aminocyclopropane-1-Carboxylate Synthase In Complex With An Amino-Oxy Analogue Of The Substrate: Implications For Substrate Binding.
Biochem. Biophys. Acta V. 1647 55 2003 Proteins & Proteomics
PubMed-ID: 12686108  |  Reference-DOI: 10.1016/S1570-9639(03)00049-9

(-) Compounds

Molecule 1 - 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE
    Chains: A
    EC Number: 4.4.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET19B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-435
    Organism Scientific: MALUS X DOMESTICA
    Organism Taxid: 3750
    Synonym: ACC SYNTHASE
    Tissue: FRUIT CORTICAL

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AAD1Ligand/Ion(2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]-METHYL-SULFONIUM
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1AAD2Ligand/Ion(2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]-METHYL-SULFONIUM
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:119 , ALA A:120 , THR A:121 , TYR A:145 , THR A:198 , ASN A:202 , ASP A:230 , ILE A:232 , TYR A:233 , SER A:270 , SER A:272 , LYS A:273 , ARG A:281 , AAD A:502 , HOH A:768BINDING SITE FOR RESIDUE PLP A 501
2AC2SOFTWAREGLN A:83 , ASP A:84 , TYR A:85 , THR A:121 , TYR A:145 , GLY A:147 , ARG A:150 , ASP A:151 , LYS A:273 , SER A:301 , PLP A:501 , MES A:601 , HOH A:619 , HOH A:624 , HOH A:685 , HOH A:717 , HOH A:776BINDING SITE FOR RESIDUE AAD A 502
3AC3SOFTWAREGLY A:44 , LEU A:45 , ALA A:46 , GLU A:47 , TYR A:145 , LYS A:273 , ARG A:407 , AAD A:502BINDING SITE FOR RESIDUE MES A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M4N)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M4N)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.1A1C_MALDO270-283  1A:270-283
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.1A1C_MALDO270-283  2A:270-283

(-) Exons   (0, 0)

(no "Exon" information available for 1M4N)

(-) 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:421
 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 d1m4na         _ A: 1-aminocyclopropane-1-carboxylate synthase (ACC synthase)                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1m4nA0         1 A:4-62,A:308-433                          1m4nA02 A:63-307 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                 1m4nA01 A:4-62,A:308-433 Aspartate Aminotransferase, domain 1                                                                  CATH domains
               Pfam domains ------------------------------------Aminotran_1_2-1m4nA01 A:40-425                                                                                                                                                                                                                                                                                                                                                                    -------- Pfam domains
         Sec.struct. author ......---------.hhhhhhhhhh...........ee........hhhhhhhhhhhh......ee..eehhhhhhhh.....hhhhhhhhhhhhhhhh......hhh.eeeeehhhhhhhhhhhhhh....eeeeee....hhhhhh......eeeeee.hhhhh...hhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh.......hhhhhhhh.......hhhh.eeeeee......hhhh.eeeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh...hhhhhhhhhhhhhhh..ee.ee.hhhh.....eeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4n A   4 LSRNAT---------YFLGWQEYEKNPYHEVHNTNGIIQMGLAENQLCFDLLESWLAKNPEAAAFKKNGESIFAELALFQDYHGLPAFKKAMVDFMAEIRGNKVTFDPNHLVLTAGATSANETFIFCLADPGEAVLIPTPYYPGFDRDLKWRTGVEIVPIHCTSSNGFQITETALEEAYQEAEKRNLRVKGVLVTNPSNPLGTTMTRNELYLLLSFVEDKGIHLISDEIYSGTAFSSPSFISVMEVLKDRNCDENSEVWQRVHVVYSLSKDLGLPGFRVGAIYSNDDMVVAAATKMSSFGLVSSQTQHLLSAMLSDKKLTKNYIAENHKRLKQRQKKLVSGLQKSGISCLNGNAGLFCWVDMRHLLRSNTFEAEMELWKKIVYEVHLNISPGSSCHCTEPGWFRVCFANLPERTLDLAMQRLKAFVGEYY 433
                                 |   -     |  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
                                 9        19
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (9, 9)

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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 Related Entries

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

UniProtKB/Swiss-Prot
        1A1C_MALDO | P37821: 1b8g 1m7y 1ynu 3piu

(-) Related Entries Specified in the PDB File

1b8g 1B8G CONTAINS THE NATIVE STRUCTURE OF APPLE ACC SYNTHASE