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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF ALLIINASE FROM GARLIC
 
Authors :  E. B. Kuettner, R. Hilgenfeld, M. S. Weiss
Date :  24 Apr 02  (Deposition) - 11 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Egf-Like Domain, Plp Type 1, Chloride Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. B. Kuettner, R. Hilgenfeld, M. S. Weiss
The Active Principle Of Garlic At Atomic Resolution
J. Biol. Chem. V. 277 46402 2002
PubMed-ID: 12235163  |  Reference-DOI: 10.1074/JBC.M208669200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALLIIN LYASE
    Chains: A, B
    EC Number: 4.4.1.4
    Organism Common: GARLIC
    Organism Scientific: ALLIUM SATIVUM
    Organism Taxid: 4682
    Other Details: BULB
    Synonym: ALLIINASE, CYSTEINE SULPHOXIDE LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 28)

Asymmetric/Biological Unit (8, 28)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL2Ligand/IonCHLORIDE ION
3DHA1Ligand/Ion2-AMINO-ACRYLIC ACID
4EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5FUC2Ligand/IonALPHA-L-FUCOSE
6NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
7PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
8SO411Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:146 , THR A:148 , ALA A:149 , FUC A:501 , NAG A:502 , HOH A:1202 , HOH A:1309BINDING SITE FOR RESIDUE NAG A 500
02AC2SOFTWARENAG A:500 , NAG A:502 , HOH A:1325 , HOH A:1330 , HOH A:1345BINDING SITE FOR RESIDUE FUC A 501
03AC3SOFTWARENAG A:500 , FUC A:501 , BMA A:503 , HOH A:1358BINDING SITE FOR RESIDUE NAG A 502
04AC4SOFTWARENAG A:502BINDING SITE FOR RESIDUE BMA A 503
05AC5SOFTWAREASN A:328 , GLN A:408 , PHE A:411 , NAG A:505 , HOH A:1328BINDING SITE FOR RESIDUE NAG A 504
06AC6SOFTWARENAG A:504BINDING SITE FOR RESIDUE NAG A 505
07AC7SOFTWAREHOH A:1366 , ASN B:146 , THR B:148 , FUC B:501BINDING SITE FOR RESIDUE NAG B 500
08AC8SOFTWAREGLU A:170 , TYR A:174 , ASN B:276 , LYS B:280 , NAG B:500BINDING SITE FOR RESIDUE FUC B 501
09AC9SOFTWAREASN B:328 , GLN B:408 , PHE B:411 , NAG B:503 , HOH B:1374BINDING SITE FOR RESIDUE NAG B 502
10BC1SOFTWARENAG B:502BINDING SITE FOR RESIDUE NAG B 503
11BC2SOFTWARELYS A:237 , GLU A:348 , ARG B:384BINDING SITE FOR RESIDUE SO4 A 904
12BC3SOFTWAREARG A:323 , HOH A:1236 , HOH A:1310BINDING SITE FOR RESIDUE SO4 A 905
13BC4SOFTWAREALA A:120 , ALA A:121 , LYS A:122 , LYS A:239 , HOH A:1094BINDING SITE FOR RESIDUE SO4 A 906
14BC5SOFTWARETHR A:310 , MET A:311 , HOH A:1306BINDING SITE FOR RESIDUE SO4 A 907
15BC6SOFTWAREGLU A:71 , LYS A:321 , THR A:407 , GLN A:408 , HOH A:1075 , HOH A:1096 , HOH A:1101 , HOH A:1145 , HOH A:1308BINDING SITE FOR RESIDUE SO4 A 910
16BC7SOFTWAREARG A:355 , MET A:356 , HOH A:1376BINDING SITE FOR RESIDUE SO4 A 911
17BC8SOFTWAREPHE A:93 , PHE A:94 , SER A:98 , ASN A:99 , PHE A:100BINDING SITE FOR RESIDUE CL A 1001
18BC9SOFTWARELYS B:74 , GLN B:75 , HIS B:76 , LYS B:77 , GLU B:78 , HOH B:1117BINDING SITE FOR RESIDUE SO4 B 901
19CC1SOFTWARETRP B:370 , GLU B:371 , ARG B:426 , HOH B:1166 , HOH B:1269 , HOH B:1408 , HOH B:1409BINDING SITE FOR RESIDUE SO4 B 902
20CC2SOFTWAREHIS B:161 , ALA B:187 , LYS B:308 , ARG B:354 , HOH B:1017 , HOH B:1103 , HOH B:1157 , HOH B:1208BINDING SITE FOR RESIDUE SO4 B 903
21CC3SOFTWAREGLU B:114 , ALA B:120 , ALA B:121 , LYS B:122 , LYS B:239 , HOH B:1246BINDING SITE FOR RESIDUE SO4 B 908
22CC4SOFTWARELYS B:367 , TYR B:399 , HOH B:1165 , HOH B:1334BINDING SITE FOR RESIDUE SO4 B 909
23CC5SOFTWAREPHE B:93 , PHE B:94 , SER B:98 , ASN B:99 , PHE B:100BINDING SITE FOR RESIDUE CL B 1002
24CC6SOFTWAREGLY A:131 , VAL A:132 , THR A:133 , TYR A:165 , THR A:203 , ASN A:207 , ASP A:225 , VAL A:227 , TYR A:228 , THR A:248 , SER A:250 , LYS A:251 , ARG A:259 , TYR B:92BINDING SITE FOR RESIDUE PLP A 600
25CC7SOFTWARETYR A:92 , THR A:279 , GLU A:283 , HOH A:1371 , SER B:63 , GLY B:64 , TYR B:165 , GLU B:170 , GLN B:388 , ARG B:401BINDING SITE FOR RESIDUE EPE A 851
26CC8SOFTWARESER A:63 , GLY A:64 , TYR A:165 , GLU A:170 , GLN A:388 , ARG A:401 , HOH A:1274 , HOH A:1363 , HOH A:1374 , TYR B:92 , THR B:279 , GLU B:283BINDING SITE FOR RESIDUE EPE A 852
27CC9SOFTWARETYR A:92 , GLY B:131 , VAL B:132 , THR B:133 , TYR B:165 , THR B:203 , ASN B:207 , ASP B:225 , VAL B:227 , TYR B:228 , THR B:248 , SER B:250 , LYS B:251 , ARG B:259 , DHA B:850BINDING SITE FOR RESIDUE PLP B 600
28DC1SOFTWARETYR A:92 , GLY B:64 , TYR B:165 , ASN B:207 , TYR B:228 , LYS B:251 , TYR B:363 , ARG B:401 , PLP B:600 , HOH B:1380BINDING SITE FOR RESIDUE DHA B 850

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:20 -A:39
2A:41 -A:50
3A:44 -A:57
4A:368 -A:376
5B:20 -B:39
6B:41 -B:50
7B:44 -B:57
8B:368 -B:376

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asn A:95 -Pro A:96
2Ala A:162 -Pro A:163
3Ser A:204 -Pro A:205
4Asn A:207 -Pro A:208
5Asn B:95 -Pro B:96
6Ala B:162 -Pro B:163
7Ser B:204 -Pro B:205
8Asn B:207 -Pro B:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LK9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_1PS00022 EGF-like domain signature 1.ALLN1_ALLSA77-88
 		  2A:39-50
B:39-50

(-) Exons   (0, 0)

(no "Exon" information available for 1LK9)

(-) Sequences/Alignments

Asymmetric/Biological 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:425
 aligned with ALLN1_ALLSA | Q01594 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:425
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458     
          ALLN1_ALLSA    39 KMTWTMKAAEEAEAVANINCSEHGRAFLDGIISEGSPKCECNTCYTGPDCSEKIQGCSADVASGDGLFLEEYWKQHKEASAVLVSPWHRMSYFFNPVSNFISFELEKTIKELHEVVGNAAAKDRYIVFGVGVTQLIHGLVISLSPNMTATPDAPESKVVAHAPFYPVFREQTKYFNKKGYVWAGNAANYVNVSNPEQYIEMVTSPNNPEGLLRHAVIKGCKSIYDMVYYWPHYTPIKYKADEDILLFTMSKFTGHSGSRFGWALIKDESVYNNLLNYMTKNTEGTPRETQLRSLKVLKEVVAMVKTQKGTMRDLNTFGFKKLRERWVNITALLDQSDRFSYQELPQSEYCNYFRRMRPPSPSYAWVKCEWEEDKDCYQTFQNGRINTQNGVGFEASSRYVRLSLIKTQDDFDQLMYYLKDMVKAK 463
               SCOP domains d1lk9a_ A: Alliinase                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1lk9A01 A:2-100 Alliin lyase; domain 1                                                             1lk9A02 A:101-310 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                             1lk9A03 A:311-423 Aspartate Aminotransferase, domain 1                                                           -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh......ee......ee..ee..ee...ee.....ee.....ee.....hhhhhhhhh.hhhhhheee.................hhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhh....eeeeee.hhhh...hhh.eeeeee.................eeeee..................eeeeehhhhh.hhhhh.eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....eee......eee....eee.....eeeeee.hhhhhhhhhhhhhh.ee.ee.hhhh....eeeee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------EGF_1       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lk9 A   1 KMTWTMKAAEEAEAVANINCSEHGRAFLDGIISEGSPKCECNTCYTGPDCSEKIQGCSADVASGDGLFLEEYWKQHKEASAVLVSPWHRMSYFFNPVSNFISFELEKTIKELHEVVGNAAAKDRYIVFGVGVTQLIHGLVISLSPNMTATPDAPESKVVAHAPFYPVFREQTKYFDKKGYVWAGNAANYVNVSNPEQYIEMVTSPNNPEGLLRHAVIKGCKSIYDMVYYWPHYTPIKYKADEDILLFTMSKFTGHSGSRFGWALIKDESVYNNLLNYMTKNTEGTPRETQLRSLKVLKEVVAMVKTQKGTMRDLNTFGFKKLRERWVNITALLDQSDRFSYQELPQSEYCNYFRRMRPPSPSYAWVKCEWEEDKDCYQTFQNGRINTQNGVGFEASSRYVRLSLIKTQDDFDQLMYYLKDMVKAK 425
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420     


Chain B from PDB  Type:PROTEIN  Length:427
 aligned with ALLN1_ALLSA | Q01594 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:427
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       
          ALLN1_ALLSA    39 KMTWTMKAAEEAEAVANINCSEHGRAFLDGIISEGSPKCECNTCYTGPDCSEKIQGCSADVASGDGLFLEEYWKQHKEASAVLVSPWHRMSYFFNPVSNFISFELEKTIKELHEVVGNAAAKDRYIVFGVGVTQLIHGLVISLSPNMTATPDAPESKVVAHAPFYPVFREQTKYFNKKGYVWAGNAANYVNVSNPEQYIEMVTSPNNPEGLLRHAVIKGCKSIYDMVYYWPHYTPIKYKADEDILLFTMSKFTGHSGSRFGWALIKDESVYNNLLNYMTKNTEGTPRETQLRSLKVLKEVVAMVKTQKGTMRDLNTFGFKKLRERWVNITALLDQSDRFSYQELPQSEYCNYFRRMRPPSPSYAWVKCEWEEDKDCYQTFQNGRINTQNGVGFEASSRYVRLSLIKTQDDFDQLMYYLKDMVKAKRK 465
               SCOP domains d1lk9b_ B: Alliinase                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -1lk9B01 B:2-100 Alliin lyase; domain 1                                                             1lk9B02 B:101-310 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                             1lk9B03 B:311-423 Aspartate Aminotransferase, domain 1                                                           ---- CATH domains
           Pfam domains (1) -EGF_alliinase-1lk9B01 B:2-57                            -Alliinase_C-1lk9B03 B:59-422                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) -EGF_alliinase-1lk9B02 B:2-57                            -Alliinase_C-1lk9B04 B:59-422                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhh......ee......ee..ee..ee...ee.....ee.....ee.....hhhhhhhhh.hhhhhheee.................hhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhh....eeeeee.hhhh...hhh.eeeeee.................eeeee..................eeeeehhhhh.hhhhh.eeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....eee......eee....eee.....eeeeee.hhhhhhhhhhhhhh.ee.ee.hhhh....eeeee...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------EGF_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lk9 B   1 KMTWTMKAAEEAEAVANINCSEHGRAFLDGIISEGSPKCECNTCYTGPDCSEKIQGCSADVASGDGLFLEEYWKQHKEASAVLVSPWHRMSYFFNPVSNFISFELEKTIKELHEVVGNAAAKDRYIVFGVGVTQLIHGLVISLSPNMTATPDAPESKVVAHAPFYPVFREQTKYFDKKGYVWAGNAANYVNVSNPEQYIEMVTSPNNPEGLLRHAVIKGCKSIYDMVYYWPHYTPIKYKADEDILLFTMSKFTGHSGSRFGWALIKDESVYNNLLNYMTKNTEGTPRETQLRSLKVLKEVVAMVKTQKGTMRDLNTFGFKKLRERWVNITALLDQSDRFSYQELPQSEYCNYFRRMRPPSPSYAWVKCEWEEDKDCYQTFQNGRINTQNGVGFEASSRYVRLSLIKTQDDFDQLMYYLKDMVKAKRK 427
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: EGF (60)
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALLN1_ALLSA | Q01594)
molecular function
    GO:0047654    alliin lyase activity    Catalysis of the reaction: an S-alkyl-L-cysteine S-oxide = an alkyl sulfenate + 2-aminoacrylate.
    GO:0016846    carbon-sulfur lyase activity    Catalysis of the elimination of hydrogen sulfide or substituted H2S.
    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.
cellular component
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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  1lk9
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  ALLN1_ALLSA | Q01594
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALLN1_ALLSA | Q01594: 2hor 2hox

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LK9)