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(-) Description

Title :  E. COLI METHIONINE AMINOPEPTIDASE MN-FORM WITH INHIBITOR B23
 
Authors :  Q. -Z. Ye
Date :  12 Jun 07  (Deposition) - 01 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Aminopeptidase, Hydrolase, Dinuclear, Mn(Ii)-Form, Enzyme- Inhibitor Complex, Metalloenzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Q. Ma, S. X. Xie, Q. Q. Huang, F. J. Nan, T. D. Hurley, Q. Z. Ye
Structural Analysis Of Inhibition Of E. Coli Methionine Aminopeptidase: Implication Of Loop Flexibility In Selective Inhibition Of Bacterial Enzymes.
Bmc Struct. Biol. V. 7 84 2007
PubMed-ID: 18093325  |  Reference-DOI: 10.1186/1472-6807-7-84
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE
    ChainsA
    EC Number3.4.11.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEMEX-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMAP
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymMAP, PEPTIDASE M

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1B231Ligand/Ion5-(2-NITROPHENYL)-2-FUROIC ACID
2MN2Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:108 , HIS A:171 , GLU A:204 , GLU A:235 , MN A:301 , B23 A:400BINDING SITE FOR RESIDUE MN A 300
2AC2SOFTWAREASP A:97 , ASP A:108 , GLU A:235 , MN A:300 , B23 A:400 , HOH A:510BINDING SITE FOR RESIDUE MN A 301
3AC3SOFTWAREASN A:74 , VAL A:76 , SER A:231 , HOH A:527BINDING SITE FOR RESIDUE NA A 500
4AC4SOFTWARECYS A:59 , TYR A:62 , TYR A:65 , CYS A:70 , ASP A:97 , ASP A:108 , HIS A:171 , PHE A:177 , HIS A:178 , GLU A:204 , TRP A:221 , GLU A:235 , MN A:300 , MN A:301BINDING SITE FOR RESIDUE B23 A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q92)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:180 -Pro A:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q92)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAP_1PS00680 Methionine aminopeptidase subfamily 1 signature.MAP1_ECOLI168-186  1A:168-186

(-) Exons   (0, 0)

(no "Exon" information available for 2Q92)

(-) 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:262
 aligned with MAP1_ECOLI | P0AE18 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:262
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
           MAP1_ECOLI     2 AISIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHD 263
               SCOP domains d2q92a_ A: Methionine aminopeptidase                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2q92A00 A:2-263 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee...hhhhh....eeee..eee..............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..ee.....eee......eeeee................eeee..eee.....eee......eee.....eee..eeeee...eeee...........eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q92 A   2 AISIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHD 263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q92)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAP1_ECOLI | P0AE18)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  3.4.11.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        MAP1_ECOLI | P0AE181c21 1c22 1c23 1c24 1c27 1mat 1xnz 1yvm 2bb7 2evc 2evm 2evo 2gg0 2gg2 2gg3 2gg5 2gg7 2gg8 2gg9 2ggb 2ggc 2gtx 2gu4 2gu5 2gu6 2gu7 2mat 2p98 2p99 2p9a 2q93 2q94 2q95 2q96 3d27 3mat 4mat 4z7m

(-) Related Entries Specified in the PDB File

1xnz E. COLI METHIONINE AMINOPEPTIDASE MN(II) FORM IN COMPLEX WITH 5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC ACID
2evc E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH 5-(2- (TRIFLUOROMETHYL)PHENYL)FURAN-2-CARBOXYLIC ACID
2evm E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH 5-(2,5- DICHLOROPHENYL)FURAN-2-CARBOXYLIC ACID
2gtx E. COLI MONONUCLEAR METHIONINE AMINOPEPTIDASE CATALYSIS
2q93 E. COLI METHIONINE AMINOPEPTIDASE MN-FORM WITH INHIBITOR B21
2q94 E. COLI METHIONINE AMINOPEPTIDASE MN-FORM WITH INHIBITOR A04
2q95 E. COLI METHIONINE AMINOPEPTIDASE MN-FORM WITH INHIBITOR A05
2q96 E. COLI METHIONINE AMINOPEPTIDASE MN-FORM WITH INHIBITOR A18