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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S228A MUTANT OF THE AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS
 
Authors :  N. J. Ataie, Q. Q. Hoang, M. P. D. Zahniser, A. Milne, G. A. Petsko, D. Ringe
Date :  22 Oct 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.22
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Beta, Aminopeptidase, Hydrolase, Metal-Binding, Protease, Secreted, Zinc, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Ataie, Q. Q. Hoang, M. P. Zahniser, Y. Tu, A. Milne, G. A. Petsko, D. Ringe
Zinc Coordination Geometry And Ligand Binding Affinity: The Structural And Kinetic Analysis Of The Second-Shell Serine 228 Residue And The Methionine 180 Residue Of The Aminopeptidase From Vibrio Proteolyticus.
Biochemistry V. 47 7673 2008
PubMed-ID: 18576673  |  Reference-DOI: 10.1021/BI702188E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIAL LEUCYL AMINOPEPTIDASE
    Atcc: 15338
    Chains: A
    EC Number: 3.4.11.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 107-397
    Gene: AAP
    Mutation: YES
    Organism Scientific: VIBRIO PROTEOLYTICUS
    Organism Taxid: 671
    Strain: DSM 30189 / IFO 13287 / LMG 3772 / NCIMB 1326

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
2SCN2Ligand/IonTHIOCYANATE ION
3VAL1Mod. Amino AcidVALINE
4ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:117 , GLU A:152 , HIS A:256 , VAL A:299BINDING SITE FOR RESIDUE ZN A 292
2AC2SOFTWAREHIS A:97 , ASP A:117 , ASP A:179 , VAL A:299BINDING SITE FOR RESIDUE ZN A 293
3AC3SOFTWARETHR A:257 , THR A:258 , GLN A:259BINDING SITE FOR RESIDUE NA A 294
4AC4SOFTWAREGLY A:72 , HOH A:449BINDING SITE FOR RESIDUE NA A 295
5AC5SOFTWARETHR A:38 , TYR A:73 , ASN A:74 , HOH A:479BINDING SITE FOR RESIDUE NA A 296
6AC6SOFTWARETHR A:194 , THR A:202 , GLN A:203 , LEU A:262 , HOH A:343BINDING SITE FOR RESIDUE SCN A 297
7AC7SOFTWAREGLN A:7 , ALA A:12 , TRP A:13 , HOH A:375 , HOH A:461BINDING SITE FOR RESIDUE SCN A 298
8AC8SOFTWAREHIS A:97 , ASP A:117 , GLU A:151 , GLU A:152 , ASP A:179 , MET A:180 , CYS A:227 , HIS A:256 , ZN A:292 , ZN A:293 , HOH A:405BINDING SITE FOR RESIDUE VAL A 299

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:117 -Asp A:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B3V)

(-) Exons   (0, 0)

(no "Exon" information available for 3B3V)

(-) 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:292
 aligned with AMPX_VIBPR | Q01693 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:304
                                   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       406    
           AMPX_VIBPR   107 MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACSDHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATGDTPTPGNQLEDGV 410
               SCOP domains d3b3va_ A: Aminopeptidase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3b3vA00 A:1-291 Zn peptidases                                                                                                                                                                                                                                                                      ------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeee....eeeeeeeeeee....................hhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee............eeee....hhhhhhhhhhhhhhhh....eeee.......hhhhhhhh...ee.ee..hhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhh..------------. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b3v A   1 MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACADHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATG------------V 299
                                    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|        -   |
                                                                                                                                                                                                                                                                                                                            291          299
   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  (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  (0, 0)

(no "Pfam Domain" information available for 3B3V)

(-) 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 2prq 3b35 3b3c 3b3s 3b3t 3b3w 3b7i 3fh4 3vh9

(-) Related Entries Specified in the PDB File

3b35 CRYSTAL STRUCTURE OF M180A MUTANT OF AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS
3b3c CRYSTAL STRUCTURE OF M180A MUTANT OF AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS IN COMPLEX WITH LEUCINE PHOSPHONIC ACID
3b3s CRYSTAL STRUCTURE OF M180A MUTANT OF AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS IN COMPLEX WITH LEUCINE
3b3t CRYSTAL STRUCTURE OF D118N MUTANT OF AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS
3b3w CRYSTAL STRUCTURE OF S228A MUTANT OF AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS IN COMPLEX WITH LEUCINE