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(-) Description

Title :  MOLECULAR STRUCTURE OF LEUCINE AMINOPEPTIDASE AT 2.7-ANGSTROMS RESOLUTION
 
Authors :  S. K. Burley, P. R. David, A. Taylor, W. N. Lipscomb
Date :  01 Aug 90  (Deposition) - 15 Oct 91  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Hydrolase(Alpha-Aminoacylpeptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Burley, P. R. David, A. Taylor, W. N. Lipscomb
Molecular Structure Of Leucine Aminopeptidase At 2. 7-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 87 6878 1990
PubMed-ID: 2395881  |  Reference-DOI: 10.1073/PNAS.87.17.6878
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOSOL AMINOPEPTIDASE
    ChainsA
    EC Number3.4.11.1
    EngineeredYES
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (6x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:255 , ASP A:332 , GLU A:334 , ZN A:489BINDING SITE FOR RESIDUE ZN A 488
2AC2SOFTWARELYS A:250 , ASP A:255 , ASP A:273 , GLU A:334 , ZN A:488BINDING SITE FOR RESIDUE ZN A 489

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LAP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:470 -Pro A:471

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOSOL_APPS00631 Cytosol aminopeptidase signature.AMPL_BOVIN362-369  1A:330-337
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOSOL_APPS00631 Cytosol aminopeptidase signature.AMPL_BOVIN362-369  6A:330-337

(-) Exons   (13, 13)

Asymmetric Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000078601ENSBTAE00000063203chr6:37961794-37961895102AMPL_BOVIN1-34341A:1-22
1.2ENSBTAT000000078602ENSBTAE00000063205chr6:37964129-37964244116AMPL_BOVIN35-73391A:3-41 (gaps)39
1.3ENSBTAT000000078603ENSBTAE00000308864chr6:37965550-3796560455AMPL_BOVIN73-91191A:41-5919
1.4ENSBTAT000000078604ENSBTAE00000063209chr6:37966063-37966168106AMPL_BOVIN92-127361A:60-9536
1.5ENSBTAT000000078605ENSBTAE00000063210chr6:37967574-37967733160AMPL_BOVIN127-180541A:95-14854
1.6ENSBTAT000000078606ENSBTAE00000063212chr6:37969197-37969361165AMPL_BOVIN180-235561A:148-20356
1.7ENSBTAT000000078607ENSBTAE00000063213chr6:37971885-37972043159AMPL_BOVIN235-288541A:203-25654
1.8ENSBTAT000000078608ENSBTAE00000063215chr6:37977709-37977833125AMPL_BOVIN288-330431A:256-29843
1.9ENSBTAT000000078609ENSBTAE00000063217chr6:37978975-3797906389AMPL_BOVIN330-359301A:298-32730
1.10ENSBTAT0000000786010ENSBTAE00000308863chr6:37979919-37980021103AMPL_BOVIN360-394351A:328-36235
1.11ENSBTAT0000000786011ENSBTAE00000063220chr6:37984212-3798429180AMPL_BOVIN394-420271A:362-38827
1.12ENSBTAT0000000786012ENSBTAE00000063222chr6:37986042-37986151110AMPL_BOVIN421-457371A:389-42537
1.13ENSBTAT0000000786013ENSBTAE00000063223chr6:37986603-37987164562AMPL_BOVIN457-519631A:425-48460

(-) 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:481
 aligned with AMPL_BOVIN | P00727 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:484
                                    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       472       482       492       502       512    
           AMPL_BOVIN    33 TKGLVLGIYSKEKEEDEPQFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHEDFPSVVVVGLGKKTAGIDEQENWHEGKENIRAAVAAGCRQIQDLEIPSVEVDPCGDAQAAAEGAVLGLYEYDDLKQKRKVVVSAKLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSASIKTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPNASEPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYAHTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAHLDIAGVMTNKDEVPYLRKGMAGRPTRTLIEFLFRFSQ 516
               SCOP domains d1lapa2 A:1   -159 Leucine aminopeptidase (Aminopeptidase A), N-terminal domain                                                                                d1lapa1 A:160-484 Leucine aminopeptidase, C-terminal domain                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1lapA01 A:1   -165 Leucine Aminopeptidase, subunit E, domain 1                                                                                                       1lapA02 A:166-483 Zn peptidases                                                                                                                                                                                                                                                                                               - CATH domains
               Pfam domains ----Peptida   se_M17_N-1lapA01 A:5-137                                                                                                   --------------------------Peptidase_M17-1lapA02 A:164-477                                                                                                                                                                                                                                                                                           ------- Pfam domains
         Sec.struct. author ..eeeeee...---......hhhhhhhhhhh.hhhhhhhhhhh.......eeeeeeee..eeeeeeee.......ee....eehhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..............eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhh......eeeeeeee.........eeeee.eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..........eeee.....eeee....hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eee...hhhhhhhhh......ee.......hhhhhhhhhhhh......eeeee.hhh.ee.........ee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOSOL_--------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.2  PDB: A:3-41 (gaps)           ------------------Exon 1.4  PDB: A:60-95              ----------------------------------------------------Exon 1.6  PDB: A:148-203 UniProt: 180-235               ----------------------------------------------------Exon 1.8  PDB: A:256-298 UniProt: 288-330  -----------------------------Exon 1.10  PDB: A:328-362          --------------------------Exon 1.12  PDB: A:389-425            ----------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3           -----------------------------------Exon 1.5  PDB: A:95-148 UniProt: 127-180              ------------------------------------------------------Exon 1.7  PDB: A:203-256 UniProt: 235-288             -----------------------------------------Exon 1.9  PDB: A:298-327      ----------------------------------Exon 1.11  PDB: A:362-388  ------------------------------------Exon 1.13  PDB: A:425-484 UniProt: 457-519 [INCOMPLETE]      Transcript 1 (2)
                 1lap A   1 TKGLVLGIYSK---EDEPQFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHEDFPSVVVVGLGKKTAGIDEQENWHEGKENIRAAVAAGCRQIQDLEIPSVEVDPCGDAQAAAEGAVLGLYEYDDLKQKRKVVVSAKLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSASIKTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPNASEPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYAHTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAHLDIAGVMTNKDEVPYLRKGMAGRPTRTLIEFLFRFSQ 484
                                    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       430       440       450       460       470       480    
                                     11  15                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: MACRO (14)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMPL_BOVIN | P00727)
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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008235    metalloexopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of 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: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.
biological process
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPL_BOVIN | P007271bll 1bpm 1bpn 1lam 1lan 1lcp 2ewb 2j9a

(-) Related Entries Specified in the PDB File

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