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Title :   CRYSTAL STRUCTURE OF METHIONINE AMINO PEPTIDASE IN COMPLEX WITH N-CYCLOPENTYL-N-(THIAZOL-2-YL)OXALAMIDE

Authors :   W. -J. Huang

Date :   31 Oct 05 (Deposition) - 28 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Methionine Aminopeptidase, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. X. Xie, W. J. Huang, Z. Q. Ma, M. Huang, R. P. Hanzlik, Q. Z. Ye
Structural Analysis Of Metalloform-Selective Inhibition Of Methionine Aminopeptidase.
Acta Crystallogr. , Sect. D V. 62 425 2006
PubMed-ID: 16552144 | Reference-DOI: 10.1107/S0907444906003878
(for further references see the PDB file header)

Molecule 1 - METHIONINE AMINOPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.11.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEMEX-1
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAP
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	MAP, PEPTIDASE M

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CO	6	Ligand/Ion	COBALT (II) ION
2	CT0	2	Ligand/Ion	N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	CT0	1	Ligand/Ion	N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	CT0	1	Ligand/Ion	N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:97 , ASP A:108 , GLU A:235 , CO A:902 , HOH A:1042 , HOH A:1043	BINDING SITE FOR RESIDUE CO A 901
2	AC2	SOFTWARE	ASP A:108 , HIS A:171 , THR A:202 , GLU A:204 , GLU A:235 , CO A:901 , HOH A:1043	BINDING SITE FOR RESIDUE CO A 902
3	AC3	SOFTWARE	HIS A:79 , CT0 A:503 , HOH A:1039 , HOH A:1040 , HOH A:1041	BINDING SITE FOR RESIDUE CO A 903
4	AC4	SOFTWARE	ASP B:97 , ASP B:108 , GLU B:235 , CO B:905 , HOH B:1022 , HOH B:1023	BINDING SITE FOR RESIDUE CO B 904
5	AC5	SOFTWARE	ASP B:108 , HIS B:171 , THR B:202 , GLU B:204 , GLU B:235 , CO B:904 , HOH B:1022	BINDING SITE FOR RESIDUE CO B 905
6	AC6	SOFTWARE	HIS B:79 , CT0 B:502 , HOH B:1019 , HOH B:1020 , HOH B:1021	BINDING SITE FOR RESIDUE CO B 906
7	AC7	SOFTWARE	CYS B:59 , TYR B:62 , TYR B:65 , CYS B:70 , HIS B:79 , HIS B:178 , CO B:906 , HOH B:1019 , HOH B:1020 , HOH B:1021	BINDING SITE FOR RESIDUE CT0 B 502
8	AC8	SOFTWARE	CYS A:59 , TYR A:62 , TYR A:65 , CYS A:70 , HIS A:79 , HIS A:178 , CO A:903 , HOH A:1031 , HOH A:1039 , HOH A:1040 , HOH A:1041	BINDING SITE FOR RESIDUE CT0 A 503

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

Asymmetric Unit

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAP_1	PS00680	Methionine aminopeptidase subfamily 1 signature.	MAP1_ECOLI	168-186	2	A:168-186 B:168-186

Biological Unit 1 (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 -

Biological Unit 2 (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	- B:168-186

(no "Exon" information available for 2EVO)

Asymmetric 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:260
 aligned with MAP1_ECOLI | P0AE18 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:260
                                    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
           MAP1_ECOLI     4 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHD 263
               SCOP domains d2evoa_ A: Methionine aminopeptidase                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2evoA00 A:4-263 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
                 2evo A   4 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHD 263
                                    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

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with MAP1_ECOLI | P0AE18 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:260
                                    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
           MAP1_ECOLI     4 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHD 263
               SCOP domains d2evob_ B: Methionine aminopeptidase                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2evoB00 B:4-263 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee...hhhhh....eeee..eee..............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..ee.....eee......eeeee................eeee..eee.....eee......eee.....eee..eeeeee..eeee...........eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ----------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2evo B   4 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHD 263
                                    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

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 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 [TaxId: 562] (30)

1a	d2evoa_	A:
1b	d2evob_	B:

Asymmetric 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. Organism_taxid: 562. (23)

1a	2evoA00	A:4-263
1b	2evoB00	B:4-263

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	Cis Peptide Bonds
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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