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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PRODUCT BOUND METHIONINE AMINOPEPTIDASE TYPE 1C FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  A. Addlagatta, M. L. Quillin, O. Omotoso, J. O. Liu, B. W. Matthews
Date :  13 Jan 05  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Pita Bread Fold, Complexed With Two Cobalt And Methionine, C285 Modification By Oxidized Beta-Mercapto Ethanol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Addlagatta, M. L. Quillin, O. Omotoso, J. O. Liu, B. W. Matthews
Identification Of An Sh3-Binding Motif In A New Class Of Methionine Aminopeptidases From Mycobacterium Tuberculosis Suggests A Mode Of Interaction With The Ribosome.
Biochemistry V. 44 7166 2005
PubMed-ID: 15882055  |  Reference-DOI: 10.1021/BI0501176
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MAP, MAPB
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: MAP, PEPTIDASE M

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CO2Ligand/IonCOBALT (II) ION
3K1Ligand/IonPOTASSIUM ION
4MET1Mod. Amino AcidMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:142 , HIS A:205 , THR A:236 , GLU A:238 , GLU A:269 , CO A:402 , MET A:500BINDING SITE FOR RESIDUE CO A 401
2AC2SOFTWAREASP A:131 , ASP A:142 , GLU A:269 , CO A:401 , MET A:500BINDING SITE FOR RESIDUE CO A 402
3AC3SOFTWARESER A:107 , LEU A:108 , ASN A:109 , VAL A:111 , THR A:265 , HOH A:570BINDING SITE FOR RESIDUE K A 403
4AC4SOFTWARETYR A:97 , PHE A:100 , CYS A:105 , ASP A:131 , THR A:133 , ASP A:142 , HIS A:205 , PHE A:211 , HIS A:212 , GLU A:238 , TRP A:255 , GLU A:269 , CO A:401 , CO A:402 , HOH A:767BINDING SITE FOR RESIDUE MET A 500
5AC5SOFTWAREHIS A:270 , THR A:283 , CYS A:284BINDING SITE FOR RESIDUE BME A 425

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YJ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YJ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YJ3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAP_1PS00680 Methionine aminopeptidase subfamily 1 signature.MAP12_MYCTO202-220  1A:202-220
MAP12_MYCTU202-220  1A:202-220

(-) Exons   (0, 0)

(no "Exon" information available for 1YJ3)

(-) 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:283
 aligned with MAP12_MYCTO | P9WK18 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:283
                                                                                                                                                                                                                                                                                                                   285 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 | 
          MAP12_MYCTO     4 RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------1yj3A01 A:40-283 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..ee............eeee..eee.............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..ee.....ee..........ee................eeee..eee.....eee......eee.....eee..eeeee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj3 A   4 RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCLM 500
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 ||
                                                                                                                                                                                                                                                                                                                   285|
                                                                                                                                                                                                                                                                                                                    500


Chain A from PDB  Type:PROTEIN  Length:283
 aligned with MAP12_MYCTU | P9WK19 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:283
                                                                                                                                                                                                                                                                                                                   285 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 | 
          MAP12_MYCTU     4 RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------1yj3A01 A:40-283 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..ee............eeee..eee.............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..ee.....ee..........ee................eeee..eee.....eee......eee.....eee..eeeee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj3 A   4 RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCLM 500
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 ||
                                                                                                                                                                                                                                                                                                                   285|
                                                                                                                                                                                                                                                                                                                    500
   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  (0, 0)

(no "SCOP Domain" information available for 1YJ3)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YJ3)

(-) Gene Ontology  (14, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAP12_MYCTO | P9WK18)
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   (MAP12_MYCTU | P9WK19)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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: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:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    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:0006555    methionine metabolic process    The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    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:0035551    protein initiator methionine removal involved in protein maturation    Removal of the initiating methionine or formylmethionine residue from a protein that contributes to protein maturation, the attainment of the full functional capacity of 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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  1yj3
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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
        MAP12_MYCTO | P9WK18: 1y1n 3iu7 3iu8 3iu9 3pka 3pkb 3pkc 3pkd 3pke 3ror 4idy 4iec 4if7 4ook
        MAP12_MYCTU | P9WK19: 1y1n 3iu7 3iu8 3iu9 3pka 3pkb 3pkc 3pkd 3pke 3ror 4idy 4iec 4if7 4ook

(-) Related Entries Specified in the PDB File

1y1n THE SAME PROTEIN IN THE APO FORM