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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCCOCUS AUREUS IN COMPLEX WITH AN AMINOKETONE INHIBITOR 54135.
 
Authors :  A. Douangamath, G. E. Dale, A. D'Arcy, C. Oefner
Date :  09 Sep 03  (Deposition) - 16 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A
Keywords :  Pita Bread Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Douangamath, G. E. Dale, A. D'Arcy, M. Almstetter, R. Eckl, A. Frutos-Hoener, B. Henkel, K. Illgen, S. Nerdinger, H. Schulz, A. Macsweeney, M. Thormann, A. Treml, S. Pierau, S. Wadman, C. Oefner
Crystal Structures Of Staphylococcusaureus Methionine Aminopeptidase Complexed With Keto Heterocycle And Aminoketone Inhibitors Reveal The Formation Of A Tetrahedral Intermediate.
J. Med. Chem. V. 47 1325 2004
PubMed-ID: 14998322  |  Reference-DOI: 10.1021/JM034188J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONYL AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDS56-RBSII
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: AUREUS MU50

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CO2Ligand/IonCOBALT (II) ION
3M1C1Ligand/Ion(3S)-3-AMINO-1-(CYCLOPROPYLAMINO)HEPTANE-2,2-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:104 , HIS A:168 , GLU A:202 , GLU A:233 , CO A:1002 , M1C A:3001BINDING SITE FOR RESIDUE CO A 1001
2AC2SOFTWAREASP A:93 , ASP A:104 , GLU A:233 , CO A:1001 , M1C A:3001BINDING SITE FOR RESIDUE CO A 1002
3AC3SOFTWAREHIS A:151 , LYS A:160 , VAL A:161 , SER A:210 , HOH A:3155BINDING SITE FOR RESIDUE ACT A 2001
4AC4SOFTWAREHIS A:58 , HOH A:3157BINDING SITE FOR RESIDUE ACT A 2002
5AC5SOFTWAREHIS A:76 , ASP A:93 , ASP A:104 , HIS A:168 , GLU A:202 , GLU A:233 , CO A:1001 , CO A:1002 , HOH A:3008 , HOH A:3034BINDING SITE FOR RESIDUE M1C A 3001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:177 -Pro A:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QXW)

(-) Exons   (0, 0)

(no "Exon" information available for 1QXW)

(-) 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:249
 aligned with MAP1_STAA1 | P0A080 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           MAP1_STAA1     1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI 249
               SCOP domains d1qxwa_ A: Methionine aminopeptidase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qxwA00 A:1-251 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhh.......................................................hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh............................................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qxw A   1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     ||  
                                                                                                                                                                                                                                                                               246|  
                                                                                                                                                                                                                                                                                249  


Chain A from PDB  Type:PROTEIN  Length:249
 aligned with MAP1_STAAM | P0A078 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           MAP1_STAAM     1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI 249
               SCOP domains d1qxwa_ A: Methionine aminopeptidase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qxwA00 A:1-251 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhh.......................................................hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh............................................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qxw A   1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     ||  
                                                                                                                                                                                                                                                                               246|  
                                                                                                                                                                                                                                                                                249
   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) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QXW)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAP1_STAA1 | P0A080)
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:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from 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: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:0070084    protein initiator methionine removal    The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A   (MAP1_STAAM | P0A078)
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:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from 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: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:0070084    protein initiator methionine removal    The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MAP1_STAA1 | P0A080: 1qxy 1qxz
        MAP1_STAAM | P0A078: 1qxy 1qxz

(-) Related Entries Specified in the PDB File

1qxy 1qxz