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(-) Description

Title :  CRYSTAL STRUCTURE OF ALLIINASE FROM GARLIC- APO FORM
 
Authors :  L. J. W Shimon, A. Rabinkov, M. Wilcheck, D. Mirelman, F. Frolow
Date :  16 Jul 06  (Deposition) - 06 Feb 07  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alliinase; Garlic; Allium Sativum; Glycosylation; Plant Enzyme; Pyridoxal-5'-Phosphate; Aminoacrylate; Apo Form; , Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Shimon, A. Rabinkov, I. Shin, T. Miron, D. Mirelman, M. Wilchek, F. Frolow
Two Structures Of Alliinase From Alliium Sativum L. : Apo Form And Ternary Complex With Aminoacrylate Reaction Intermediate Covalently Bound To The Plp Cofactor.
J. Mol. Biol. V. 366 611 2007
PubMed-ID: 17174334  |  Reference-DOI: 10.1016/J.JMB.2006.11.041
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 16)

Asymmetric Unit (8, 16)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3CL2Ligand/IonCHLORIDE ION
4FUC1Ligand/IonALPHA-L-FUCOSE
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NO31Ligand/IonNITRATE ION
8SO45Ligand/IonSULFATE ION
Biological Unit 1 (7, 28)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BMA2Ligand/IonBETA-D-MANNOSE
3CL-1Ligand/IonCHLORIDE ION
4FUC2Ligand/IonALPHA-L-FUCOSE
5MAN4Ligand/IonALPHA-D-MANNOSE
6NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NO32Ligand/IonNITRATE ION
8SO410Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:146 , ALA A:149 , TYR A:174 , FUC A:501 , NAG A:503 , SO4 A:701 , HOH A:849 , HOH A:875 , HOH A:1124 , HOH A:1131BINDING SITE FOR RESIDUE NAG A 500
02AC2SOFTWAREGLU A:170 , ASN A:276 , LYS A:280 , NAG A:500 , NAG A:503 , HOH A:849 , HOH A:875 , HOH A:1137BINDING SITE FOR RESIDUE FUC A 501
03AC3SOFTWARETHR A:148 , LYS A:173 , NAG A:500 , FUC A:501 , BMA A:504 , SO4 A:701 , HOH A:849 , HOH A:991 , HOH A:1116BINDING SITE FOR RESIDUE NAG A 503
04AC4SOFTWARENAG A:503 , MAN A:505 , MAN A:506 , HOH A:1174 , HOH A:1177 , HOH A:1178 , HOH A:1201BINDING SITE FOR RESIDUE BMA A 504
05AC5SOFTWAREVAL A:391 , BMA A:504 , HOH A:995BINDING SITE FOR RESIDUE MAN A 505
06AC6SOFTWAREGLU A:114 , BMA A:504 , HOH A:876 , HOH A:1005BINDING SITE FOR RESIDUE MAN A 506
07AC7SOFTWAREASN A:328 , GLN A:408 , PHE A:411 , HOH A:942 , HOH A:1018 , HOH A:1098BINDING SITE FOR RESIDUE NAG A 555
08AC8SOFTWAREGLY A:64 , TYR A:165 , ASN A:207 , LYS A:251 , GLN A:388 , ARG A:401 , HOH A:777 , HOH A:789 , HOH A:944 , HOH A:1095 , HOH A:1185BINDING SITE FOR RESIDUE SO4 A 600
09AC9SOFTWARETYR A:92 , GLY A:131 , VAL A:132 , THR A:133 , THR A:248 , SER A:250 , ARG A:259 , HOH A:766 , HOH A:1053 , HOH A:1096BINDING SITE FOR RESIDUE SO4 A 601
10BC1SOFTWARETYR A:165 , ASP A:225 , VAL A:227 , HOH A:766 , HOH A:1095 , HOH A:1096BINDING SITE FOR RESIDUE ACT A 602
11BC2SOFTWARENAG A:500 , NAG A:503 , HOH A:1201BINDING SITE FOR RESIDUE SO4 A 701
12BC3SOFTWAREGLU A:22 , ASN A:42 , THR A:407 , GLN A:408 , ASP A:409 , HOH A:971 , HOH A:1115BINDING SITE FOR RESIDUE SO4 A 702
13BC4SOFTWARELYS A:74 , GLN A:75 , HIS A:76 , LYS A:77 , GLU A:78 , HOH A:735BINDING SITE FOR RESIDUE SO4 A 703
14BC5SOFTWAREPHE A:93 , PHE A:94 , SER A:98 , PHE A:100BINDING SITE FOR RESIDUE CL A 705
15BC6SOFTWAREGLU A:114 , HOH A:1192BINDING SITE FOR RESIDUE CL A 706
16BC7SOFTWAREHIS A:137 , PHE A:175 , LYS A:177 , HOH A:1162BINDING SITE FOR RESIDUE NO3 A 707

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:20 -A:39
2A:41 -A:50
3A:44 -A:57
4A:368 -A:376

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HOR)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HOR)

(-) 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: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 d2hora_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2horA01 A:1-100 Alliin lyase; domain 1                                                              2horA02 A:101-310 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                             2horA03 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.hhhhhh....................hhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhh...........eeeee.....hhhhhhhhhh....eeeeee.hhhh...hhh.eeeeee.................eeeee..................eeeeehhhhh.hhhhh.eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....ee.......eee....eee.....eeeeee.hhhhhhhhhhhhhh.ee.ee.hhhh....eeeee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------EGF_1       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hor 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
   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  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HOR)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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        ALLN1_ALLSA | Q01594: 1lk9 2hox

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