2EWB - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF BOVINE LENS LEUCINE AMINOPEPTIDASE IN COMPLEX WITH ZOFENOPRILAT

Authors :   V. Alterio, C. Pedone, G. De Simone

Date :   02 Nov 05 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

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

Reference :   M. Cappiello, V. Alterio, P. Amodeo, A. Del Corso, A. Scaloni, C. Pedone, R. Moschini, G. M. De Donatis, G. De Simone, U. Mura
Metal Ion Substitution In The Catalytic Site Greatly Affect The Binding Of Sulfhydryl-Containing Compounds To Leucyl Aminopeptidase.
Biochemistry V. 45 3226 2006
PubMed-ID: 16519517 | Reference-DOI: 10.1021/BI052069V

Molecule 1 - CYTOSOL AMINOPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.11.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	LENS
	Synonym	:	LEUCINE AMINOPEPTIDASE, LAP, LEUCYL AMINOPEPTIDASE, PROLINE AMINOPEPTIDASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION
4	ZED	1	Ligand/Ion	L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 36)

No.	Name	Count	Type	Full Name
1	CO3	6	Ligand/Ion	CARBONATE ION
2	MPD	24	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION
4	ZED	6	Ligand/Ion	L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:255 , ASP A:332 , GLU A:334 , ZN A:489 , ZED A:2000	BINDING SITE FOR RESIDUE ZN A 488
2	AC2	SOFTWARE	LYS A:250 , ASP A:255 , ASP A:273 , GLU A:334 , ZN A:488 , ZED A:2000	BINDING SITE FOR RESIDUE ZN A 489
3	AC3	SOFTWARE	LEU A:170 , MET A:171 , THR A:173 , ARG A:271 , MET A:274 , HOH A:2063	BINDING SITE FOR RESIDUE NA A 490
4	AC4	SOFTWARE	LYS A:250 , ALA A:333 , GLU A:334 , GLY A:335 , ARG A:336 , LEU A:360 , ZED A:2000	BINDING SITE FOR RESIDUE CO3 A 500
5	AC5	SOFTWARE	LYS A:250 , ASP A:255 , LYS A:262 , ASN A:330 , ASP A:332 , GLU A:334 , LEU A:360 , THR A:361 , GLY A:362 , ILE A:421 , ZN A:488 , ZN A:489 , CO3 A:500 , HOH A:2079 , HOH A:2396	BINDING SITE FOR RESIDUE ZED A 2000
6	AC6	SOFTWARE	ALA A:48 , TRP A:82 , ASN A:88 , HOH A:2154 , HOH A:2183 , HOH A:2283	BINDING SITE FOR RESIDUE MPD A 501
7	AC7	SOFTWARE	PRO A:44 , LEU A:46 , THR A:51 , ARG A:52 , ASP A:102 , LEU A:103 , HOH A:2086	BINDING SITE FOR RESIDUE MPD A 502
8	AC8	SOFTWARE	ASN A:176 , GLU A:177 , VAL A:317 , ARG A:319	BINDING SITE FOR RESIDUE MPD A 503
9	AC9	SOFTWARE	HIS A:233 , TYR A:234 , PRO A:244 , ASN A:295 , PHE A:349 , HOH A:2067	BINDING SITE FOR RESIDUE MPD A 504

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

Asymmetric Unit

No.	Residues
1	Arg A:470	-	Pro A:471

(no "SAP(SNP)/Variant" information available for 2EWB)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOSOL_AP	PS00631	Cytosol aminopeptidase signature.	AMPL_BOVIN	362-369	1	A:330-337

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOSOL_AP	PS00631	Cytosol aminopeptidase signature.	AMPL_BOVIN	362-369	6	A:330-337

Asymmetric Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000007860	1	ENSBTAE00000063203	chr6:37961794-37961895	102	AMPL_BOVIN	1-34	34	1	A:1-2	2
1.2	ENSBTAT00000007860	2	ENSBTAE00000063205	chr6:37964129-37964244	116	AMPL_BOVIN	35-73	39	1	A:3-41	39
1.3	ENSBTAT00000007860	3	ENSBTAE00000308864	chr6:37965550-37965604	55	AMPL_BOVIN	73-91	19	1	A:41-59	19
1.4	ENSBTAT00000007860	4	ENSBTAE00000063209	chr6:37966063-37966168	106	AMPL_BOVIN	92-127	36	1	A:60-95	36
1.5	ENSBTAT00000007860	5	ENSBTAE00000063210	chr6:37967574-37967733	160	AMPL_BOVIN	127-180	54	1	A:95-148	54
1.6	ENSBTAT00000007860	6	ENSBTAE00000063212	chr6:37969197-37969361	165	AMPL_BOVIN	180-235	56	1	A:148-203	56
1.7	ENSBTAT00000007860	7	ENSBTAE00000063213	chr6:37971885-37972043	159	AMPL_BOVIN	235-288	54	1	A:203-256	54
1.8	ENSBTAT00000007860	8	ENSBTAE00000063215	chr6:37977709-37977833	125	AMPL_BOVIN	288-330	43	1	A:256-298	43
1.9	ENSBTAT00000007860	9	ENSBTAE00000063217	chr6:37978975-37979063	89	AMPL_BOVIN	330-359	30	1	A:298-327	30
1.10	ENSBTAT00000007860	10	ENSBTAE00000308863	chr6:37979919-37980021	103	AMPL_BOVIN	360-394	35	1	A:328-362	35
1.11	ENSBTAT00000007860	11	ENSBTAE00000063220	chr6:37984212-37984291	80	AMPL_BOVIN	394-420	27	1	A:362-388	27
1.12	ENSBTAT00000007860	12	ENSBTAE00000063222	chr6:37986042-37986151	110	AMPL_BOVIN	421-457	37	1	A:389-425	37
1.13	ENSBTAT00000007860	13	ENSBTAE00000063223	chr6:37986603-37987164	562	AMPL_BOVIN	457-519	63	1	A:425-486	62

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:486
 aligned with AMPL_BOVIN | P00727 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:486
                                    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       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512      
           AMPL_BOVIN    33 TKGLVLGIYSKEKEEDEPQFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHEDFPSVVVVGLGKKTAGIDEQENWHEGKENIRAAVAAGCRQIQDLEIPSVEVDPCGDAQAAAEGAVLGLYEYDDLKQKRKVVVSAKLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSASIKTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPNASEPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYAHTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAHLDIAGVMTNKDEVPYLRKGMAGRPTRTLIEFLFRFSQDS 518
               SCOP domains d2ewba2 A:1-159 automated matches                                                                                                                              d2ewba1 A:160-486 automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2ewbA01 A:1-165 Leucine Aminopeptidase, subunit E, domain 1                                                                                                          2ewbA02 A:166-483 Zn peptidases                                                                                                                                                                                                                                                                                               --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee............hhhhhhhhhhh.hhhhhhhhhhh.......eeeeeeee..eeeeeeee.......ee....eehhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh.............eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhh......eeeeeeee.........eeeee.eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..........eeee.....eeee.....hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh.....ee.......hhhhhhhhhhhh......eeeee.hhh.ee.........ee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOSOL_----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.2  PDB: A:3-41 UniProt: 35-73   ------------------Exon 1.4  PDB: A:60-95              ----------------------------------------------------Exon 1.6  PDB: A:148-203 UniProt: 180-235               ----------------------------------------------------Exon 1.8  PDB: A:256-298 UniProt: 288-330  -----------------------------Exon 1.10  PDB: A:328-362          --------------------------Exon 1.12  PDB: A:389-425            ------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3           -----------------------------------Exon 1.5  PDB: A:95-148 UniProt: 127-180              ------------------------------------------------------Exon 1.7  PDB: A:203-256 UniProt: 235-288             -----------------------------------------Exon 1.9  PDB: A:298-327      ----------------------------------Exon 1.11  PDB: A:362-388  ------------------------------------Exon 1.13  PDB: A:425-486 UniProt: 457-519 [INCOMPLETE]        Transcript 1 (2)
                 2ewb A   1 TKGLVLGIYSKEKEEDEPQFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHEDFPSVVVVGLGKKTAGIDEQENWHEGKENIRAAVAAGCRQIQDLEIPSVEVDPCGDAQAAAEGAVLGLYEYDDLKQKRKVVVSAKLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSASIKTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPNASEPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYAHTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAHLDIAGVMTNKDEVPYLRKGMAGRPTRTLIEFLFRFSQDS 486
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480

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: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: Zn peptidases (137)

Cattle (Bos taurus) (28)

2ewbA02

A:166-483

Topology: Leucine Aminopeptidase, subunit E; domain 1 (21)

Homologous Superfamily: Leucine Aminopeptidase, subunit E, domain 1 (21)

Cattle (Bos taurus) (5)

2ewbA01

A:1-165

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

Asymmetric Unit(hide GO term definitions)

Chain A (AMPL_BOVIN | P00727)

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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0019538	protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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		Arg A:470 - Pro A:471	[ RasMol ]

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1lam	THE CRYSTAL STRUCTURE OF LEUCINE AMINOPEPTIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (13, 13)

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