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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC CHARACTERIZATION OF THE CO(II)-SUBSTITUTED TRIS-BOUND FORM OF THE AMINOPEPTIDASE FROM AEROMONAS PROTEOLYTICA
 
Authors :  P. Munih, A. Moulin, C. C. Stamper, B. Bennet, D. Ringe, G. A. Petsko, R. C. Holz
Date :  04 May 07  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Tris, X-Ray, Peptidase, Aminohydrolase, Cobalt, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Munih, A. Moulin, C. C. Stamper, B. Bennett, D. Ringe, G. A. Petsko, R. C. Holz
X-Ray Crystallographic Characterization Of The Co(Ii)-Substituted Tris-Bound Form Of The Aminopeptidase From Aeromonas Proteolytica.
J. Inorg. Biochem. V. 101 1099 2007
PubMed-ID: 17574677  |  Reference-DOI: 10.1016/J.JINORGBIO.2007.03.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIAL LEUCYL AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 107-397
    Organism Scientific: VIBRIO PROTEOLYTICUS
    Organism Taxid: 671

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:117 , GLU A:152 , HIS A:256 , CO A:502 , TRS A:840BINDING SITE FOR RESIDUE CO A 501
2AC2SOFTWAREHIS A:97 , ASP A:117 , GLU A:151 , ASP A:179 , CO A:501 , TRS A:840BINDING SITE FOR RESIDUE CO A 502
3AC3SOFTWAREHIS A:97 , ASP A:117 , GLU A:151 , GLU A:152 , ASP A:179 , TYR A:225 , CYS A:227 , PHE A:244 , CO A:501 , CO A:502 , HOH A:916BINDING SITE FOR RESIDUE TRS A 840

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:223 -A:227

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PRQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PRQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PRQ)

(-) 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:291
 aligned with AMPX_VIBPR | Q01693 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:291
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
           AMPX_VIBPR   107 MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACSDHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATG 397
               SCOP domains d2prqa_ A: Aminopeptidase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2prqA00 A:1-291 Zn peptidases                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -----------------------------------------------------------------------------------------Peptidase_M28-2prqA01 A:90-271                                                                                                                                                        -------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeeee........eeeeee....eeeeeeeeeee....................hhhhhhhhhhhhhhhhh......eeeeeeee......hhhhhhhhhhhhhh..eeeeeee............eeee....hhhhhhhhhhhhhhhh....eeee.......hhhhhhhh...eeeee..hhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2prq A   1 MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACSDHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATG 291
                                    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
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMPX_VIBPR | Q01693)
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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPX_VIBPR | Q01693: 1amp 1cp6 1ft7 1igb 1lok 1rtq 1txr 1xry 2anp 2dea 2iq6 2nyq 3b35 3b3c 3b3s 3b3t 3b3v 3b3w 3b7i 3fh4 3vh9

(-) Related Entries Specified in the PDB File

1amp NATIVE FORM OF AAP
1lok AAP WITH TRIS BOUND AT HIGH RESOLUTION (1.2 A)