2GU5 - JenaLib

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Title :   E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH NLEP, 1: 1, DI-METALATED

Authors :   Q. Z. Ye

Date :   28 Apr 06 (Deposition) - 04 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Mono-Metalated, Mononuclear, Mn(Ii)-Form, Hydrolase, Enzyme- Inhibitor Complex, Metalloenzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Z. Ye, S. X. Xie, Z. Q. Ma, M. Huang, R. P. Hanzlik
Structural Basis Of Catalysis By Monometalated Methionine Aminopeptidase.
Proc. Natl. Acad. Sci. Usa V. 103 9470 2006
PubMed-ID: 16769889 | Reference-DOI: 10.1073/PNAS.0602433103
(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 BL21(DE3)
	Expression System Plasmid	:	PGEMEX-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	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 (3, 8)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION
2	NA	2	Ligand/Ion	SODIUM ION
3	NLP	2	Ligand/Ion	(1-AMINO-PENTYL)-PHOSPHONIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	NLP	1	Ligand/Ion	(1-AMINO-PENTYL)-PHOSPHONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	NLP	1	Ligand/Ion	(1-AMINO-PENTYL)-PHOSPHONIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:108 , HIS A:171 , GLU A:204 , GLU A:235 , MN A:266 , NLP A:3808	BINDING SITE FOR RESIDUE MN A 265
2	AC2	SOFTWARE	ASP A:97 , ASP A:108 , GLU A:235 , MN A:265 , NLP A:3808	BINDING SITE FOR RESIDUE MN A 266
3	AC3	SOFTWARE	ASP B:108 , HIS B:171 , GLU B:204 , GLU B:235 , MN B:266 , NLP B:3808	BINDING SITE FOR RESIDUE MN B 265
4	AC4	SOFTWARE	ASP B:97 , ASP B:108 , GLU B:235 , MN B:265 , NLP B:3808	BINDING SITE FOR RESIDUE MN B 266
5	AC5	SOFTWARE	ASN A:74 , VAL A:76 , SER A:231 , HOH A:3829	BINDING SITE FOR RESIDUE NA A 300
6	AC6	SOFTWARE	ASN B:74 , VAL B:76 , SER B:231 , HOH B:3817	BINDING SITE FOR RESIDUE NA B 300
7	AC7	SOFTWARE	TYR A:65 , CYS A:70 , HIS A:79 , ASP A:97 , THR A:99 , ASP A:108 , HIS A:171 , PHE A:177 , HIS A:178 , GLU A:204 , GLU A:235 , MN A:265 , MN A:266	BINDING SITE FOR RESIDUE NLP A 3808
8	AC8	SOFTWARE	TYR B:62 , CYS B:70 , HIS B:79 , ASP B:97 , THR B:99 , ASP B:108 , HIS B:171 , PHE B:177 , HIS B:178 , GLU B:204 , GLU B:235 , MN B:265 , MN B:266 , HOH B:3971	BINDING SITE FOR RESIDUE NLP B 3808

(no "SS Bond" information available for 2GU5)

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 2GU5)

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 2GU5)

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:261
 aligned with MAP1_ECOLI | P0AE18 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:261
                                    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 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE 264
               SCOP domains d2gu5a_ A: Methionine aminopeptidase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2gu5A00 A:4-264 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..eeeeee..eeee...........eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gu5 A   4 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE 264
                                    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:261
 aligned with MAP1_ECOLI | P0AE18 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:261
                                    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 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE 264
               SCOP domains d2gu5b_ B: Methionine aminopeptidase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2gu5B00 B:4-264 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
                 2gu5 B   4 SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE 264
                                    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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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	d2gu5a_	A:
1b	d2gu5b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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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	2gu5A00	A:4-264
1b	2gu5B00	B:4-264

(no "Pfam Domain" information available for 2GU5)

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.

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

Biological Units
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	2gu5
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2gtx	E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH NLEP, 1: 0.25, MONO-METALATED
2gu4	E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH NLEP, 1: 0.5, DI-METALATED
2gu6	E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH NLEP, 1: 2, DI-METALATED
2gu7	E. COLI METHIONINE AMINOPEPTIDASE UNLIGANDED, 1:0.5

Description

Compounds

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

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