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Title :   NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS

Authors :   A. G. Evdokimov, M. E. Pokross, R. L. Walter, M. Mekel

Date :   23 Mar 06 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

Chains :   Asym./Biol. Unit : A

Keywords :   Methionine Amino Peptidase, Pita-Bread Fold, Map Inhibitor, Antibacterial, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Evdokimov, M. Pokross, R. L. Walter, M. Mekel, B. L. Barnett, J. Amburgey, W. L. Seibel, S. J. Soper, J. F. Djung, N. Fairweather, C. Diven, V. Rastogi, L. Grinius, C. Klanke, R. Siehnel, T. Twinem, R. Andrews, A. Curnow
Serendipitous Discovery Of Novel Bacterial Methionine Aminopeptidase Inhibitors.
Proteins V. 66 538 2007
PubMed-ID: 17120228 | Reference-DOI: 10.1002/PROT.21207
(for further references see the PDB file header)

Molecule 1 - METHIONINE AMINOPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.11.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MAP
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	MAP, PEPTIDASE M

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION
2	NA	1	Ligand/Ion	SODIUM ION
3	U17	1	Ligand/Ion	METHYL N-[(2S,3R)-3-AMINO-2-HYDROXYHEPTANOYL]-L-SERYL-L-LEUCINATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:108 , HIS A:171 , GLU A:204 , GLU A:235 , CO A:302 , U17 A:304	BINDING SITE FOR RESIDUE CO A 301
2	AC2	SOFTWARE	ASP A:97 , ASP A:108 , GLU A:235 , CO A:301 , U17 A:304	BINDING SITE FOR RESIDUE CO A 302
3	AC3	SOFTWARE	ASN A:74 , VAL A:76 , SER A:231 , HOH A:339	BINDING SITE FOR RESIDUE NA A 303
4	AC4	SOFTWARE	TYR A:62 , HIS A:79 , ASP A:97 , THR A:99 , ASP A:108 , TYR A:168 , CYS A:169 , HIS A:171 , PHE A:177 , HIS A:178 , GLU A:204 , GLU A:235 , CO A:301 , CO A:302 , HOH A:326	BINDING SITE FOR RESIDUE U17 A 304

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:180	-	Pro A:181

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAP_1	PS00680	Methionine aminopeptidase subfamily 1 signature.	MAP1_ECOLI	168-186	1	A:168-186

(no "Exon" information available for 2GGB)

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:263
 aligned with MAP1_ECOLI | P0AE18 from UniProtKB/Swiss-Prot  Length:264

    Alignment length: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   
           MAP1_ECOLI     2 AISIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE 264
               SCOP domains d2ggba_ A: Methionine aminopeptidase                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2ggbA00 A:2-264 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee...hhhhh....eeee..eee..............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...ee.....eee......eeeee................eeee..eee.....eee......eee.....eee..eeeee...eeee...........eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ggb A   2 AISIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE 264
                                    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)
		→ 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Creatinase/aminopeptidase (103)

Superfamily: Creatinase/aminopeptidase (103)

Family: Creatinase/aminopeptidase (99)

Protein domain: Methionine aminopeptidase (66)

Escherichia coli K-12 [TaxId: 83333] (9)

d2ggba_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Creatine Amidinohydrolase (114)

Homologous Superfamily: Creatinase/methionine aminopeptidase superfamily (114)

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. (9)

2ggbA00

A:2-264

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

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:180 - Pro A:181	[ RasMol ]

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2gg0	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2gg2	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2gg3	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2gg5	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2gg7	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2gg8	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2gg9	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS
2ggc	NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

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Gene Ontology (10, 10)

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