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(-) Description

Title :  STRUCTURE OF NATIVE LEUKOTRIENE A4 HYDROLASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  C. Helgstrand, M. Hasan, H. Usyal, J. Z. Haeggstrom, M. M. G. M. Thunniss
Date :  31 Aug 10  (Deposition) - 29 Dec 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Helgstrand, M. Hasan, H. Uysal, J. Z. Haeggstr, M. M. G. M. Thunnisse
A Leukotriene A(4) Hydrolase-Related Aminopeptidase From Yeast Undergoes Induced Fit Upon Inhibitor Binding.
J. Mol. Biol. V. 406 120 2011
PubMed-ID: 21146536  |  Reference-DOI: 10.1016/J.JMB.2010.11.059

(-) Compounds

Molecule 1 - LEUKOTRIENE A-4 HYDROLASE
    Chains: A
    EC Number: 3.3.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-11, PETM-30
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Fragment: RESIDUES 40-671
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: GLUTATHIONE ATTACHED AT CYS147
    Synonym: LTA-4 HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2GSH1Ligand/IonGLUTATHIONE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:273 , HIS A:330BINDING SITE FOR RESIDUE GOL A1672
2AC2SOFTWAREHIS A:340 , HIS A:344 , GLU A:363 , HOH A:2112 , HOH A:2113BINDING SITE FOR RESIDUE ZN A1673
3AC3SOFTWARELYS A:95 , HIS A:97 , ASP A:104 , CYS A:147 , ASP A:149 , PHE A:600 , LYS A:601 , LYS A:604 , PRO A:633 , ARG A:636 , LEU A:637BINDING SITE FOR RESIDUE GSH A1674

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XPY)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:53 -Pro A:54
2Glu A:134 -Pro A:135
3Glu A:186 -Ala A:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.LKHA4_YEAST337-346  1A:337-346

(-) Exons   (0, 0)

(no "Exon" information available for 2XPY)

(-) 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:628
 aligned with LKHA4_YEAST | Q10740 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:632
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669  
          LKHA4_YEAST    40 MLPLSIEQRRPSRSPEYDQSTLSNYKDFAVLHTDLNLSVSFEKSAISGSVTFQLKKLHEGKNKSDELHLDTSYLDVQEVHIDGSKADFQIEQRKEPLGSRLVINNASCNDNFTLNIQFRTTDKCTALQWLNSKQTKGGKPYVFSQLEAIHARSLFPCFDTPSVKSTFTASIESPLPVVFSGIRIEDTSKDTNIYRFEQKVPIPAYLIGIASGDLSSAPIGPRSTVYTEPFRLKDCQWEFENDVEKFIQTAEKIIFEYEWGTYDILVNVDSYPYGGMESPNMTFATPTLIAHDRSNIDVIAHELAHSWSGNLVTNCSWNHFWLNEGWTVYLERRIIGAIHGEPTRHFSALIGWSDLQNSIDSMKDPERFSTLVQNLNDNTDPDDAFSTVPYEKGFNLLFHLETILGGKAEFDPFIRHYFKKFAKKSLDTFQFLDTLYEFYPEKKEILDSVDWETWLYKPGMPPRPHFITALADNVYQLADKWVEMAQHLKTTEDFRSEFNAIDIKDFNSNQLVLFLETLTQNGHSNKKPKDFDWAKFPVASRALLDIYQDNIVKSQNAEVVFKMFKFQIFAKLQEEYKHLADWLGTVGRMKFVRPGYRLLNSVDRRLALATFDKFKDTYHPICKALVKQDLGL 671
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Peptidase_M1-2xpyA01 A:63-432                                                                                                                                                                                                                                                                                                                                                     ---------------------------------------------------------------------------Leuk-A4-hydro_C-2xpyA02 A:508-669                                                                                                                                 -- Pfam domains
         Sec.struct. author ..hhhhhh...............hhh.eeeeeeeeeeeee....eeeeeeeeeeee...........ee....eeeeeeee..ee..eee..........eee.......eeeeeeeeee......eeeehhhhh.....eeee.....hhhhh..........eeeeeeee....eee..ee..----...eeeeeeeeeehhhhh.eeee..eeeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee........ee.....eee.hhhh........hhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhh..hhhhhhh.hhhhhhhh..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpy A  40 MLPLSIEQRRPSRSPEYDQSTLSNYKDFAVLHTDLNLSVSFEKSAISGSVTFQLKKLHEGKNKSDELHLDTSYLDVQEVHIDGSKADFQIEQRKEPLGSRLVINNASCNDNFTLNIQFRTTDKCTALQWLNSKQTKGGKPYVFSQLEAIHARSLFPCFDTPSVKSTFTASIESPLPVVFSGIRIE----DTNIYRFEQKVPIPAYLIGIASGDLSSAPIGPRSTVYTEPFRLKDCQWEFENDVEKFIQTAEKIIFEYEWGTYDILVNVDSYPYGGMESPNMTFATPTLIAHDRSNIDVIAHELAHSWSGNLVTNCSWNHFWLNEGWTVYLERRIIGAIHGEPTRHFSALIGWSDLQNSIDSMKDPERFSTLVQNLNDNTDPDDAFSTVPYEKGFNLLFHLETILGGKAEFDPFIRHYFKKFAKKSLDTFQFLDTLYEFYPEKKEILDSVDWETWLYKPGMPPRPHFITALADNVYQLADKWVEMAQHLKTTEDFRSEFNAIDIKDFNSNQLVLFLETLTQNGHSNKKPKDFDWAKFPVASRALLDIYQDNIVKSQNAEVVFKMFKFQIFAKLQEEYKHLADWLGTVGRMKFVRPGYRLLNSVDRRLALATFDKFKDTYHPICKALVKQDLGL 671
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    |  229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669  
                                                                                                                                                                                                                  224  229
   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  (0, 0)

(no "SCOP Domain" information available for 2XPY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XPY)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MA (251)
(-)
Clan: TPR (230)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LKHA4_YEAST | Q10740)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0004301    epoxide hydrolase activity    Catalysis of the reaction: an epoxide + H2O = a glycol.
    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:0004463    leukotriene-A4 hydrolase activity    Catalysis of the reaction: H(2)O + leukotriene A(4) = leukotriene B(4).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:0043171    peptide catabolic process    The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LKHA4_YEAST | Q10740: 2xpz 2xq0

(-) Related Entries Specified in the PDB File

2xpz STRUCTURE OF NATIVE YEAST LTA4 HYDROLASE
2xq0 STRUCTURE OF YEAST LTA4 HYDROLASE IN COMPLEX WITH BESTATIN