1QXZ - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF S. AUREUS METHIONINE AMINOPEPTIDASE IN COMPLEX WITH A KETOHETEROCYCLE INHIBITOR 119

Authors :   A. Douangamath, G. E. Dale, A. D'Arcy, C. Oefner

Date :   09 Sep 03 (Deposition) - 16 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

Chains :   Asym./Biol. Unit : A

Keywords :   Pita Bread Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Douangamath, G. E. Dale, A. D'Arcy, M. Almstetter, R. Eckl, A. Frutos-Hoener, B. Henkel, K. Illgen, S. Nerdinger, H. Schulz, A. Macsweeney, M. Thormann, A. Treml, S. Pierau, S. Wadman, C. Oefner
Crystal Structures Of Staphylococcusaureus Methionine Aminopeptidase Complexed With Keto Heterocycle And Aminoketone Inhibitors Reveal The Formation Of A Tetrahedral Intermediate.
J. Med. Chem. V. 47 1325 2004
PubMed-ID: 14998322 | Reference-DOI: 10.1021/JM034188J
(for further references see the PDB file header)

Molecule 1 - METHIONYL AMINOPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.11.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDS56-RBSII
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	AUREUS MU50

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CO	3	Ligand/Ion	COBALT (II) ION
2	M3C	1	Ligand/Ion	(2S)-2-AMINO-4-(METHYLSULFANYL)-1-(1,3-THIAZOL-2-YL)BUTANE-1,1-DIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:108 , HIS A:171 , GLU A:204 , GLU A:235 , CO A:1002 , CO A:1003 , M3C A:2001	BINDING SITE FOR RESIDUE CO A 1001
2	AC2	SOFTWARE	ASP A:97 , ASP A:108 , GLU A:235 , CO A:1001 , M3C A:2001	BINDING SITE FOR RESIDUE CO A 1002
3	AC3	SOFTWARE	HIS A:178 , CO A:1001 , M3C A:2001 , HOH A:2070 , HOH A:2192	BINDING SITE FOR RESIDUE CO A 1003
4	AC4	SOFTWARE	HIS A:79 , ASP A:97 , ASP A:108 , HIS A:171 , HIS A:178 , GLU A:204 , PHE A:206 , GLU A:235 , CO A:1001 , CO A:1002 , CO A:1003 , HOH A:2020 , HOH A:2070 , HOH A:2192	BINDING SITE FOR RESIDUE M3C A 2001

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:180	-	Pro A:181

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

(no "PROSITE Motif" information available for 1QXZ)

(no "Exon" information available for 1QXZ)

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:249
 aligned with MAP1_STAA1 | P0A080 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          MAP1_STAA1      1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI  249
               SCOP domains d1qxza_ A: Methionine aminopeptidase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qxzA00 A:1-251 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhh.......................................................hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh............................................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qxz A    1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI  251
                              ||    12        22        32        42    ||  53        63        73        83|       94       104       114      |123       133       143       153       163       173      182A       192       202       212       222       232       242         
                              3|                                       47|                                83|                                120A                                                           182A                                                                     
                               6                                        49                                 85

Chain A from PDB  Type:PROTEIN  Length:249
 aligned with MAP1_STAAM | P0A078 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          MAP1_STAAM      1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI  249
               SCOP domains d1qxza_ A: Methionine aminopeptidase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qxzA00 A:1-251 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhh.......................................................hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh............................................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qxz A    1 MIVKTEEELQALKEIGYICAKVRNTMQAATKPGITTKELDNIAKELFEEYGAISAPIHDENFPGQTCISVNEEVAHGIPSKRVIREGDLVNIDVSALKNGYYADTGISFVVGESDDPMKQKVCDVATMAFENAIAKVKPGTKLSNIGKAVHNTARQNDLKVIKNLTGHGVGLSLHEAPAHVLNYFDPKDKTLLTEGMVLAIEPFISSNASFVTEGKNEWAFETSDKSFVAQIEHTVIVTKDGPILTTKI  251
                              ||    12        22        32        42    ||  53        63        73        83|       94       104       114      |123       133       143       153       163       173      182A       192       202       212       222       232       242         
                              3|                                       47|                                83|                                120A                                                           182A                                                                     
                               6                                        49                                 85

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/Biological 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)

Staphylococcus aureus [TaxId: 1280] (3)

d1qxza_

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)

Staphylococcus aureus. Organism_taxid: 1280. Strain: aureus mu50. (3)

1qxzA00

A:1-251

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MAP1_STAAM | P0A078)

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.

Chain A (MAP1_STAA1 | P0A080)

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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	Cis Peptide Bonds
		Ala A:180 - Pro A:181	[ RasMol ]

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	MAP1_STAA1 \| P0A080	:	1qxw 1qxy
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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