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Title :   THE PRODUCT BOUND FORM OF THE MN(II)LOADED METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS

Authors :   A. J. Copik, B. P. Nocek, S. B. Jang, S. I. Swierczek, S. Ruebush, L. Meng, V. M. D'Souza, J. W. Peters, B. Bennett, R. C. Holz

Date :   01 Jun 04 (Deposition) - 22 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

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

Reference :   A. J. Copik, B. P. Nocek, S. I. Swierczek, S. Ruebush, S. B. Jang, L. Meng, V. M. D'Souza, J. W. Peters, B. Bennett, R. C. Holz
Epr And X-Ray Crystallographic Characterization Of The Product-Bound Form Of The Mnii-Loaded Methionyl Aminopeptidase From Pyrococcus Furiosus
Biochemistry V. 44 121 2005
PubMed-ID: 15628852 | Reference-DOI: 10.1021/BI048123+
(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 Taxid	:	562
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	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, 6)

No.	Name	Count	Type	Full Name
1	MET	2	Mod. Amino Acid	METHIONINE
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MET	1	Mod. Amino Acid	METHIONINE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MET	1	Mod. Amino Acid	METHIONINE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:93 , HIS A:153 , GLU A:187 , GLU A:280 , MN A:297 , MET A:1298	BINDING SITE FOR RESIDUE MN A 296
2	AC2	SOFTWARE	ASP A:82 , ASP A:93 , GLU A:280 , MN A:296 , MET A:1298	BINDING SITE FOR RESIDUE MN A 297
3	AC3	SOFTWARE	ASP B:82 , ASP B:93 , GLU B:280 , MN B:297 , MET B:2298	BINDING SITE FOR RESIDUE MN B 296
4	AC4	SOFTWARE	ASP B:93 , HIS B:153 , GLU B:187 , GLU B:280 , MN B:296 , MET B:2298	BINDING SITE FOR RESIDUE MN B 297
5	AC5	SOFTWARE	PHE A:50 , ASN A:53 , HIS A:62 , ASP A:82 , ASP A:93 , HIS A:153 , HIS A:161 , GLU A:187 , ILE A:205 , GLU A:280 , MN A:296 , MN A:297	BINDING SITE FOR RESIDUE MET A 1298
6	AC6	SOFTWARE	PHE B:50 , ASN B:53 , HIS B:62 , ASP B:82 , ASP B:93 , HIS B:153 , HIS B:161 , GLU B:187 , ILE B:205 , GLU B:280 , MN B:296 , MN B:297	BINDING SITE FOR RESIDUE MET B 2298

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

Asymmetric Unit

No.	Residues
1	Pro A:201	-	Pro A:202
2	Pro B:201	-	Pro B:202

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAP_2	PS01202	Methionine aminopeptidase subfamily 2 signature.	MAP2_PYRFU	77-93	2	A:77-93 B:77-93

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAP_2	PS01202	Methionine aminopeptidase subfamily 2 signature.	MAP2_PYRFU	77-93	1	A:77-93 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAP_2	PS01202	Methionine aminopeptidase subfamily 2 signature.	MAP2_PYRFU	77-93	1	- B:77-93

(no "Exon" information available for 1WKM)

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:295
 aligned with MAP2_PYRFU | P56218 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     
           MAP2_PYRFU     1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
               SCOP domains d1wkma1 A:1-194,A:272-295 Methionine aminopeptidase                                                                                                                                               d1wkma2 A:195-271 Methionine aminopeptidase, insert domain                   d1wkma1                  SCOP domains
               CATH domains 1wkmA01 A:1-194,A:272-295 Creatinase/methionine aminopeptidase superfamily                                                                                                                        1wkmA02 A:195-271 'winged helix' repressor DNA binding domain                1wkmA01                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..ee....eeee..eee................eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...ee.....eee..........ee................eeee..eee.....eeeeeeeeeeee.......hhhhhhhhhhhhhhhh...ee.hhhh...hhhhhhhhhhhhhhh..eeeeeeeee.....eee..eeeee....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------MAP_2            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkm A   1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with MAP2_PYRFU | P56218 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     
           MAP2_PYRFU     1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
               SCOP domains d1wkmb1 B:1-194,B:272-295 Methionine aminopeptidase                                                                                                                                               d1wkmb2 B:195-271 Methionine aminopeptidase, insert domain                   d1wkmb1                  SCOP domains
               CATH domains 1wkmB01 B:1-194,B:272-295 Creatinase/methionine aminopeptidase superfamily                                                                                                                        1wkmB02 B:195-271 'winged helix' repressor DNA binding domain                1wkmB01                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..ee....eeee..eee................eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...ee.....eee..........ee................eeee..eee.....eeeeeeeeeeee.......hhhhhhhhhhhhhhhh...ee.hhhh...hhhhhhhhhhhhhhh..eeeeeeeee.....eee..eeeee....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------MAP_2            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkm B   1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

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(

)

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)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

1a	1wkmA01	A:1-194,A:272-295
1b	1wkmB01	B:1-194,B:272-295

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Pyrococcus furiosus. Organism_taxid: 2261. (2)

2a	1wkmA02	A:195-271
2b	1wkmB02	B:195-271

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (MAP2_PYRFU | P56218)

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.

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	MAP2_PYRFU \| P56218	:	1xgm 1xgn 1xgo 1xgs 2dfi

Description

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Ligands, Modified Residues, Ions (2, 6)

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