3FMR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN ENCEPHALITOZOON CUNICULI METHIONINE AMINOPEPTIDASE TYPE 2 WITH ANGIOGENESIS INHIBITOR TNP470 BOUND

Authors :   J. J. Alvarado, M. Russell, A. Zhang, J. Adams, R. Toro, S. K. Burley, L. M S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)

Date :   22 Dec 08 (Deposition) - 13 Jan 09 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.89

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

Keywords :   Methionine Aminopeptidase Type2, Metap2, Metap2 Tnp470 Complex, Encephalitozoon Cuniculi, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Aminopeptidase, Cobalt, Hydrolase, Metal-Binding, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Alvarado, A. Nemkal, J. M. Sauder, M. Russell, D. E. Akiyoshi, W. Shi, S. C. Almo, L. M. Weiss
Structure Of A Microsporidian Methionine Aminopeptidase Typ 2 Complexed With Fumagillin And Tnp-470.
Mol. Biochem. Parasitol. V. 168 158 2009
PubMed-ID: 19660503 | Reference-DOI: 10.1016/J.MOLBIOPARA.2009.07.008

Molecule 1 - METHIONINE AMINOPEPTIDASE 2
	Chains	:	A, B
	EC Number	:	3.4.11.18
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PBAC2
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	ECU10_0750, MAP2
	Organism Scientific	:	ENCEPHALITOZOON CUNICULI
	Organism Taxid	:	6035
	Strain	:	GB-M1
	Synonym	:	METAP 2, MAP-2, PEPTIDASE M 2

		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 (3, 10)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION
2	SO4	4	Ligand/Ion	SULFATE ION
3	TN4	2	Ligand/Ion	(1R,2S,3S,4R)-4-HYDROXY-2-METHOXY-4-METHYL-3-[(2R,3R)-2-METHYL-3-(3-METHYLBUT-2-EN-1-YL)OXIRAN-2-YL]CYCLOHEXYL (CHLOROACETYL)CARBAMATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	SO4	3	Ligand/Ion	SULFATE ION
3	TN4	1	Ligand/Ion	(1R,2S,3S,4R)-4-HYDROXY-2-METHOXY-4-METHYL-3-[(2R,3R)-2-METHYL-3-(3-METHYLBUT-2-EN-1-YL)OXIRAN-2-YL]CYCLOHEXYL (CHLOROACETYL)CARBAMATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	TN4	1	Ligand/Ion	(1R,2S,3S,4R)-4-HYDROXY-2-METHOXY-4-METHYL-3-[(2R,3R)-2-METHYL-3-(3-METHYLBUT-2-EN-1-YL)OXIRAN-2-YL]CYCLOHEXYL (CHLOROACETYL)CARBAMATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:141 , HIS A:210 , GLU A:243 , GLU A:339 , FE A:402 , TN4 A:451	BINDING SITE FOR RESIDUE FE A 401
02	AC2	SOFTWARE	ASP A:130 , ASP A:141 , GLU A:339 , FE A:401	BINDING SITE FOR RESIDUE FE A 402
03	AC3	SOFTWARE	HIS A:109 , ASP A:206 , LEU A:207 , HIS A:208 , HIS A:218 , GLU A:243 , TYR A:324 , FE A:401	BINDING SITE FOR RESIDUE TN4 A 451
04	AC4	SOFTWARE	ARG A:77 , ARG A:296	BINDING SITE FOR RESIDUE SO4 A 501
05	AC5	SOFTWARE	LYS A:88 , ARG B:77 , ARG B:296	BINDING SITE FOR RESIDUE SO4 A 502
06	AC6	SOFTWARE	LYS A:305 , ARG B:91 , PHE B:215	BINDING SITE FOR RESIDUE SO4 A 503
07	AC7	SOFTWARE	ASP B:141 , HIS B:210 , GLU B:243 , GLU B:339 , FE B:402 , TN4 B:451	BINDING SITE FOR RESIDUE FE B 401
08	AC8	SOFTWARE	ASP B:130 , ASP B:141 , GLU B:339 , FE B:401	BINDING SITE FOR RESIDUE FE B 402
09	AC9	SOFTWARE	PHE B:97 , HIS B:109 , ASP B:206 , LEU B:207 , HIS B:208 , ILE B:217 , HIS B:218 , GLU B:243 , TYR B:324 , FE B:401	BINDING SITE FOR RESIDUE TN4 B 451
10	BC1	SOFTWARE	LYS B:268 , LYS B:271	BINDING SITE FOR RESIDUE SO4 B 504

(no "SS Bond" information available for 3FMR)

Asymmetric Unit

No.	Residues
1	Gly A:219	-	Gly A:220
2	Pro A:257	-	Pro A:258
3	Pro B:257	-	Pro B:258

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MAP2_ENCCU_001 *	L	288	F	MAP2_ENCCU	---	---	A/B	L	288	F
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MAP2_ENCCU_001 *	L	288	F	MAP2_ENCCU	---	---	A	L	288	F
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MAP2_ENCCU_001 *	L	288	F	MAP2_ENCCU	---	---	B	L	288	F
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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_ENCCU	125-141	2	A:125-141 B:125-141

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_ENCCU	125-141	1	A:125-141 -

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_ENCCU	125-141	1	- B:125-141

(no "Exon" information available for 3FMR)

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:356
 aligned with MAP2_ENCCU | Q8SR45 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:356
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      
           MAP2_ENCCU     3 CILLNQAEELPIEFLPKDGVYGKGKLFDSRNMEIENFTESDILQDARRAAEAHRRARYRVQSIVRPGITLLEIVRSIEDSTRTLLKGERNNGIGFPAGMSMNSCAAHYTVNPGEQDIVLKEDDVLKIDFGTHSDGRIMDSAFTVAFKENLEPLLVAAREGTETGIKSLGVDVRVCDIGRDINEVISSYEVEIGGRMWPIRPISDLHGHSISQFRIHGGISIPAVNNRDTTRIKGDSFYAVETFATTGKGSIDDRPPCSHFVLNTYKSRKLFNKDLIKVYEFVKDSLGTLPFSPRHLDYYGLVKGGSLKSVNLLTMMGLLTPYPPLNDIDGCKVAQFEHTVYLSEHGKEVLTRGDDY 358
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------3fmrA01 A:43-250,A:331-354 Creatinase/methionine aminopeptidase superfamily                                                                                                                                     3fmrA02 A:251-330 'winged helix' repressor DNA binding domain                   3fmrA01                 ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................ee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhh.eeeeeeeee..eee.................eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee..eeee.ee.....eeee.........ee..............eeeeeeeeee......ee.....eeee.........hhhhhhhhhhhhhhh.....hhhhhhh.......hhhhhhhhhhh..eeee..ee......eeeeeeeeeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------MAP_2            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmr A   3 CILLNQAEELPIEFLPKDGVYGKGKLFDSRNMEIENFTESDILQDARRAAEAHRRARYRVQSIVRPGITLLEIVRSIEDSTRTLLKGERNNGIGFPAGMSMNSCAAHYTVNPGEQDIVLKEDDVLKIDFGTHSDGRIMDSAFTVAFKENLEPLLVAAREGTETGIKSLGVDVRVCDIGRDINEVISSYEVEIGGRMWPIRPISDLHGHSISQFRIHGGISIPAVNNRDTTRIKGDSFYAVETFATTGKGSIDDRPPCSHFVLNTYKSRKLFNKDLIKVYEFVKDSLGTLPFSPRHLDYYGLVKGGSLKSVNLLTMMGLLTPYPPLNDIDGCKVAQFEHTVYLSEHGKEVLTRGDDY 358
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain B from PDB  Type:PROTEIN  Length:356
 aligned with MAP2_ENCCU | Q8SR45 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:356
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      
           MAP2_ENCCU     3 CILLNQAEELPIEFLPKDGVYGKGKLFDSRNMEIENFTESDILQDARRAAEAHRRARYRVQSIVRPGITLLEIVRSIEDSTRTLLKGERNNGIGFPAGMSMNSCAAHYTVNPGEQDIVLKEDDVLKIDFGTHSDGRIMDSAFTVAFKENLEPLLVAAREGTETGIKSLGVDVRVCDIGRDINEVISSYEVEIGGRMWPIRPISDLHGHSISQFRIHGGISIPAVNNRDTTRIKGDSFYAVETFATTGKGSIDDRPPCSHFVLNTYKSRKLFNKDLIKVYEFVKDSLGTLPFSPRHLDYYGLVKGGSLKSVNLLTMMGLLTPYPPLNDIDGCKVAQFEHTVYLSEHGKEVLTRGDDY 358
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------3fmrB01 B:43-250,B:331-354 Creatinase/methionine aminopeptidase superfamily                                                                                                                                     3fmrB02 B:251-330 'winged helix' repressor DNA binding domain                   3fmrB01                 ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................ee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhh.eeeeeeeee..eee.................eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee..eeee.ee.....eeee.........ee..............eeeeeeeeee......ee.....eeee.........hhhhhhhhhhhhhhh.....hhhhhhhh......hhhhhhhhhhh..eeee..ee......eeeeeeeeeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------MAP_2            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmr B   3 CILLNQAEELPIEFLPKDGVYGKGKLFDSRNMEIENFTESDILQDARRAAEAHRRARYRVQSIVRPGITLLEIVRSIEDSTRTLLKGERNNGIGFPAGMSMNSCAAHYTVNPGEQDIVLKEDDVLKIDFGTHSDGRIMDSAFTVAFKENLEPLLVAAREGTETGIKSLGVDVRVCDIGRDINEVISSYEVEIGGRMWPIRPISDLHGHSISQFRIHGGISIPAVNNRDTTRIKGDSFYAVETFATTGKGSIDDRPPCSHFVLNTYKSRKLFNKDLIKVYEFVKDSLGTLPFSPRHLDYYGLVKGGSLKSVNLLTMMGLLTPYPPLNDIDGCKVAQFEHTVYLSEHGKEVLTRGDDY 358
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

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 3FMR)

(no "Pfam Domain" information available for 3FMR)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MAP2_ENCCU | Q8SR45)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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 Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:219 - Gly A:220	[ RasMol ]
		Pro A:257 - Pro A:258	[ RasMol ]
		Pro B:257 - Pro B:258	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	3fmr
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	MAP2_ENCCU \| Q8SR45	:	3fm3 3fmq

3fm3	CRYSTAL STRUCTURE OF AN ENCEPHALITOZOON CUNICULI METHIONINE AMINOPEPTIDASE TYPE 2, APO FORM
3fmq	CRYSTAL STRUCTURE OF AN ENCEPHALITOZOON CUNICULI METHIONINE AMINOPEPTIDASE TYPE 2 WITH ANGIOGENESIS INHIBITOR FUMAGILLIN BOUND RELATED ID: NYSGXRC-9201A RELATED DB: TARGETDB

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