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(-) Description

Title :  CRYSTAL STRUCTURE OF DNPEP, ZNMG FORM
 
Authors :  P. D. Kiser, Y. Chen, K. Palczewski
Date :  29 Dec 11  (Deposition) - 29 Feb 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Alpha-Beta-Alpha Sandwich, Aspartyl Aminopeptidase, Binuclear Metal Center, M18 Peptidase, Mh Clan, Tetrahedral Aminopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chen, E. R. Farquhar, M. R. Chance, K. Palczewski, P. D. Kiser
Insights Into Substrate Specificity And Metal Activation Of Mammalian Tetrahedral Aspartyl Aminopeptidase.
J. Biol. Chem. V. 287 13356 2012
PubMed-ID: 22356908  |  Reference-DOI: 10.1074/JBC.M112.347518

(-) Compounds

Molecule 1 - ASPARTYL AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: DNPEP
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: DNPEP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:285 , GLU A:323 , HIS A:461 , MG A:502 , HOH A:608 , HOH A:698BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS A:115 , ASP A:285 , ASP A:367 , ZN A:501 , HOH A:609 , HOH A:698BINDING SITE FOR RESIDUE MG A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VAT)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:285 -Asn A:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VAT)

(-) 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:458
 aligned with DNPEP_BOVIN | Q2HJH1 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:469
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462         
          DNPEP_BOVIN     3 GRARKEAVQAAARELLKFVNRSPSPFHAVAECRSRLLQAGFHELKETESWDIKPESKYFLTRNSSTIIAFAVGGQYVPGNGFSLIGAHTDSPCLRVKRRSRRSQVGFQQVGVETYGGGIWSTWFDRDLTLAGRVIVKCPTSGRLEQRLVHVDRPILRIPHLAIHLQRNVNENFGPNMEMHLVPILATSIQEELEKGTPEPGPLNATDERHHSVLTSLLCAHLGLSPEDILEMELCLADTQPAVLGGAYEEFIFAPRLDNLHSCFCALQALIDSCSAPASLAADPHVRMIALYDNEEVGSESAQGAQSLLTELVLRRISASPQHLTAFEEAIPKSYMISADMAHAVHPNYLDKHEENHRPLFHKGPVIKVNSKQRYASNAVSEALIREVASSVGVPLQDLMVRNDSPCGTTIGPILASRLGLRVLDLGSPQLAMHSIRETACTTGVLQTITLFKGFFELFPSLSRSLLVD 471
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..ee.............eeeeee...eeeeeee.........eeeeeee....eeeeeeeeeeee..eeeeeeeee...hhhhhh...eeeeeeeeee......eeeeeee...........hhhhh.................eeeehhhhhhhh.-----------...hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhh..eeeeeee.hhhhh.........hhhhhhhhhhhh.....hhhhhhh...eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhh.eeeeee.eee......eeeehhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vat A  28 GRARKEAVQAAARELLKFVNRSPSPFHAVAECRSRLLQAGFHELKETESWDIKPESKYFLTRNSSTIIAFAVGGQYVPGNGFSLIGAHTDSPCLRVKRRSRRSQVGFQQVGVETYGGGIWSTWFDRDLTLAGRVIVKCPTSGRLEQRLVHVDRPILRIPHLAIHLQRNVNENFGPNMEMHLVPILATSIQEELEKG-----------ERHHSVLTSLLCAHLGLSPEDILEMELCLADTQPAVLGGAYEEFIFAPRLDNLHSCFCALQALIDSCSAPASLAADPHVRMIALYDNEEVGSESAQGAQSLLTELVLRRISASPQHLTAFEEAIPKSYMISADMAHAVHPNYLDKHEENHRPLFHKGPVIKVNSKQRYASNAVSEALIREVASSVGVPLQDLMVRNDSPCGTTIGPILASRLGLRVLDLGSPQLAMHSIRETACTTGVLQTITLFKGFFELFPSLSRSLLVD 496
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     |   -       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487         
                                                                                                                                                                                                                             223         235
   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 3VAT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VAT)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (DNPEP_BOVIN | Q2HJH1)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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  3vat
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  DNPEP_BOVIN | Q2HJH1
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  3.4.11.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNPEP_BOVIN | Q2HJH1: 3var

(-) Related Entries Specified in the PDB File

3var ZNZN FORM