1Y1N - JenaLib

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Title :   IDENTIFICATION OF SH3 MOTIF IN M. TUBERCULOSIS METHIONINE AMINOPEPTIDASE SUGGESTS A MODE OF INTERACTION WITH THE RIBOSOME

Authors :   A. Addlagatta, M. L. Quillin, O. Omotoso, J. O. Liu, B. W. Matthews

Date :   18 Nov 04 (Deposition) - 24 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.51

Chains :   Asym./Biol. Unit : A

Keywords :   Methionine Aminopeptidase; Mtmetap1B; Pxxp; Sh3; Ribosome; L24, 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)

Molecule 1 - METHIONINE AMINOPEPTIDASE 1B
	Chains	:	A
	EC Number	:	3.4.11.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A MTMETAP1B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MAP, MAPB
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Other Details	:	N-TERMINAL HIS-TAG WAS KEPT DURING CRYSTALLIZATION BUT IS NOT VISIBLE IN THE ELECRON DENSITY MAPS
	Synonym	:	MAP; PEPTIDASE M

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:107 , LEU A:108 , ASN A:109 , VAL A:111 , THR A:265 , HOH A:590	BINDING SITE FOR RESIDUE K A 403

(no "SS Bond" information available for 1Y1N)

(no "Cis Peptide Bond" information available for 1Y1N)

(no "SAP(SNP)/Variant" information available for 1Y1N)

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.	MAP12_MYCTO	202-220	1	A:202-220
1	MAP_1	PS00680	Methionine aminopeptidase subfamily 1 signature.	MAP12_MYCTU	202-220	1	A:202-220

(no "Exon" information available for 1Y1N)

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:282
 aligned with MAP12_MYCTO | P9WK18 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:282
                                    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 285
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------1y1nA01 A:40-283 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..ee............eeee..eee.............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh......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
                 1y1n A   4 RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL 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

Chain A from PDB  Type:PROTEIN  Length:282
 aligned with MAP12_MYCTU | P9WK19 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:282
                                    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 285
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------1y1nA01 A:40-283 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..ee............eeee..eee.............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee.....ee..........ee................eeee..eee.....eee......eee.....eee..eeeee....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ----------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y1n A   4 RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL 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

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 '\|'

(no "SCOP Domain" information available for 1Y1N)

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)

Mycobacterium tuberculosis. Organism_taxid: 1773. (2)

1y1nA01

A:40-283

(no "Pfam Domain" information available for 1Y1N)

Asymmetric/Biological Unit(hide GO term definitions)

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.

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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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