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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HATCHING ENZYME ZHE1 FROM THE ZEBRAFISH DANIO RERIO
 
Authors :  M. Tanokura, A. Okada, K. Nagata, S. Yasumasu, J. Ohtsuka, I. Iuchi
Date :  08 Feb 10  (Deposition) - 08 Sep 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Metalloprotease, Hatching Enzyme, Astacin, Metal-Binding, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Okada, K. Sano, K. Nagata, S. Yasumasu, J. Ohtsuka, A. Yamamura, K. Kubota, I. Iuchi, M. Tanokura
Crystal Structure Of Zebrafish Hatching Enzyme 1 From The Zebrafish Danio Rerio
J. Mol. Biol. V. 402 865 2010
PubMed-ID: 20727360  |  Reference-DOI: 10.1016/J.JMB.2010.08.023

(-) Compounds

Molecule 1 - LOC792177 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 65-263
    Gene: ZHE1
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: HATCHING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:71 , HIS A:99 , GLU A:100 , HIS A:103 , HIS A:109 , ZN A:201 , HOH A:213 , HOH A:242 , HOH A:269 , HOH A:307 , HOH A:329BINDING SITE FOR RESIDUE SO4 A 200
2AC2SOFTWAREHIS A:99 , HIS A:103 , HIS A:109 , SO4 A:200BINDING SITE FOR RESIDUE ZN A 201
3AC3SOFTWAREGLN A:59 , ALA A:60 , ASP A:61 , HOH A:254 , HOH A:292BINDING SITE FOR RESIDUE EDO A 202
4AC4SOFTWAREGLU A:6 , ASP A:7 , GLN A:48 , LEU A:185 , LYS A:187 , ILE A:190BINDING SITE FOR RESIDUE EDO A 203

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:10
2A:50 -A:199
3A:71 -A:91

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:172 -Pro A:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LQB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LQB)

(-) Exons   (0, 0)

(no "Exon" information available for 3LQB)

(-) 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:198
 aligned with Q1LW01_DANRE | Q1LW01 from UniProtKB/TrEMBL  Length:263

    Alignment length:198
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
         Q1LW01_DANRE    66 ALICEDKSCFWKKNANNIVEVPYVVSGEFSINDKSVIANAISIFHAQTCIRFVPRSIQADYLSIENKDGCYSAIGRTGGKQVVSLNRKGCVYSGIAQHELNHALGFYHEQSRSDRDQYVRINWNNISPGMAYNFLKQKTNNQNTPYDYGSLMHYGKTAFAIQPGLETITPIPDENVQIGQRQGLSKIDILRINKLYGC 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------Astacin-3lqbA01 A:11-199                                                                                                                                                                      Pfam domains
         Sec.struct. author ..................eeeeeee....hhhhhhhhhhhhhhhhhhh.eeeee......eeeee....eee.......eeeeee......hhhhhhhhhhhhhh..hhhhh.hhhh.eee.hhhh...hhhhhh................................eee..............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lqb A   2 ALICEDKSCFWKKNANNIVEVPYVVSGEFSINDKSVIANAISIFHAQTCIRFVPRSIQADYLSIENKDGCYSAIGRTGGKQVVSLNRKGCVYSGIAQHELNHALGFYHEQSRSDRDQYVRINWNNISPGMAYNFLKQKTNNQNTPYDYGSLMHYGKTAFAIQPGLETITPIPDENVQIGQRQGLSKIDILRINKLYGC 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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  (0, 0)

(no "SCOP Domain" information available for 3LQB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LQB)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q1LW01_DANRE | Q1LW01)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0035188    hatching    The emergence of an immature organism from a protective structure.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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