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Title :   STRUCTURE OF THE M1 ALANYLAMINOPEPTIDASE FROM MALARIA COMPLEXED WITH THE PHOSPHINATE DIPEPTIDE ANALOG

Authors :   S. Mcgowan, C. J. Porter, A. M. Buckle, J. C. Whisstock

Date :   27 Aug 08 (Deposition) - 27 Jan 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Aminopeptidase, Metal-Binding, Metalloprotease, Protease, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Mcgowan, C. J. Porter, J. Lowther, C. M. Stack, S. J. Golding, T. S. Skinner-Adams, K. R. Trenholme, F. Teuscher, S. M. Donnelly, J. Grembecka, A. Mucha, P. Kafarski, R. Degori, A. M. Buckle, D. L. Gardiner, J. C. Whisstock, J. P. Dalton
Structural Basis For The Inhibition Of The Essential Plasmodium Falciparum M1 Neutral Aminopeptidase
Proc. Natl. Acad. Sci. Usa V. 106 2537 2009
PubMed-ID: 19196988 | Reference-DOI: 10.1073/PNAS.0807398106

Molecule 1 - M1 FAMILY AMINOPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRCHIS2B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 195 TO 1084
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	186763
	Strain	:	D10
	Synonym	:	PFA-M1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 11)

No.	Name	Count	Type	Full Name
1	BEY	1	Ligand/Ion	(2S)-3-[(R)-[(1S)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]-2-BENZYLPROPANOIC ACID
2	GOL	5	Ligand/Ion	GLYCEROL
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:496 , HIS A:500 , GLU A:519 , BEY A:1085	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	ZN A:1 , GLN A:317 , GLU A:319 , VAL A:459 , GLY A:460 , ALA A:461 , MET A:462 , GLU A:463 , ARG A:489 , VAL A:493 , HIS A:496 , GLU A:497 , HIS A:500 , GLU A:519 , TYR A:575 , TYR A:580 , MET A:1034 , HOH A:1544 , HOH A:1545	BINDING SITE FOR RESIDUE BEY A1085
03	AC3	SOFTWARE	HOH A:19 , LYS A:479 , TYR A:880 , HIS A:886 , VAL A:887 , ASP A:888 , GLN A:891 , MET A:892 , ARG A:895 , TYR A:925 , HOH A:1513	BINDING SITE FOR RESIDUE GOL A1086
04	AC4	SOFTWARE	HOH A:100 , HOH A:103 , HOH A:1473 , HOH A:1542 , HOH A:1543	BINDING SITE FOR RESIDUE MG A 10
05	AC5	SOFTWARE	TYR A:765 , CYS A:768 , THR A:769 , TYR A:772 , TYR A:823 , SER A:826 , PRO A:828 , HOH A:1502	BINDING SITE FOR RESIDUE GOL A 2
06	AC6	SOFTWARE	HOH A:105 , HIS A:653 , LYS A:676 , TYR A:741 , ASN A:835 , HOH A:1417	BINDING SITE FOR RESIDUE GOL A 3
07	AC7	SOFTWARE	HOH A:62 , VAL A:459 , GLY A:460 , ASN A:471 , ASN A:473 , SER A:474 , ARG A:489 , ARG A:997	BINDING SITE FOR RESIDUE GOL A 4
08	AC8	SOFTWARE	ILE A:483 , LEU A:930 , THR A:931 , SER A:934 , THR A:966 , ARG A:969 , HOH A:1116 , HOH A:1154 , HOH A:1369	BINDING SITE FOR RESIDUE GOL A 5
09	AC9	SOFTWARE	HOH A:26 , GLY A:250 , HOH A:1099 , HOH A:1214 , HOH A:1536	BINDING SITE FOR RESIDUE MG A 7
10	BC1	SOFTWARE	HOH A:1177 , HOH A:1537 , HOH A:1538 , HOH A:1539 , HOH A:1540	BINDING SITE FOR RESIDUE MG A 8
11	BC2	SOFTWARE	GLU A:957 , HOH A:1541	BINDING SITE FOR RESIDUE MG A 9

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:319	-	Ala A:320

(no "SAP(SNP)/Variant" information available for 3EBI)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	AMP1_PLAFQ	493-502	1	A:493-502

(no "Exon" information available for 3EBI)

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:889
 aligned with AMP1_PLAFQ | O96935 from UniProtKB/Swiss-Prot  Length:1085

    Alignment length:889
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075         
          AMP1_PLAFQ    196 PKIHYRKDYKPSGFIINNVTLNINIHDNETIVRSVLDMDISKHNVGEDLVFDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVIIHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTADKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPHLKPCYLFAVVAGDLKHLSATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVGHEYFHNYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVDLLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILGEEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLWFSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGLINPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDNLTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFNLTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVLADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMRTLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFELYDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPNDIRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKLWNKLDTKRQELMLNEMNTMLQEPNISNNLKEYLLRLTNK 1084
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeeee....eeeeeeeeeee........eeee....eeeeeee..........eee...eeee.........eeeeeeeee.........eeeee..eeeee...................eeeeeeeeee.....eeee..eeeeeeee...eeeeeeeeeeee......eeee.eeeeeeeee......eeeeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeeeee............eeeee............hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...................eeeeeeeeee....eeeeeeeeee.............eeeeeeeee..........eeeee...eeeeee.......eee.........eee....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhh....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhh..hhhhhhhh..........hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ebi A  196 PKIHYRKDYKPSGFIINQVTLNINIHDQETIVRSVLDMDISKHNVGEDLVFDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVIIHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTADKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPPLKPCYLFAVVAGDLKHLSATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVGHEYFHQYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVDLLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILGEEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLWFSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGLINPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDQLTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFQLTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVLADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMRTLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFELYDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPNDIRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKLWNKLDTKRQELMLNEMNTMLQEPQISNNLKEYLLRLTNK 1084
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075

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 3EBI)

(no "CATH Domain" information available for 3EBI)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AMP1_PLAFQ | O96935)

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:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds 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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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/Biological Unit
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	Cis Peptide Bonds
		Glu A:319 - Ala A:320	[ RasMol ]

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	3.4.11.-
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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