3H8E - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   LOW PH NATIVE STRUCTURE OF LEUCINE AMINOPEPTIDASE FROM PSEUDOMONAS PUTIDA

Authors :   A. Kale, B. W. Dijkstra, T. Sonke, A. M. W. H Thunnissen

Date :   29 Apr 09 (Deposition) - 14 Apr 10 (Release) - 02 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)
Biol. Unit 2: A,B  (1x)

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

Reference :   A. Kale, T. Pijning, T. Sonke, B. W. Dijkstra, A. M. Thunnissen
Crystal Structure Of The Leucine Aminopeptidase From Pseudomonas Putida Reveals The Molecular Basis For Its Enantioselectivity And Broad Substrate Specificity.
J. Mol. Biol. V. 398 703 2010
PubMed-ID: 20359484 | Reference-DOI: 10.1016/J.JMB.2010.03.042

Molecule 1 - CYTOSOL AMINOPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRPLAP
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PEPA
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Strain	:	ATCC12633
	Synonym	:	LEUCINE AMINOPEPTIDASE, LAP, LEUCYL AMINOPEPTIDASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3H8E)

(no "Site" information available for 3H8E)

(no "SS Bond" information available for 3H8E)

Asymmetric Unit

No.	Residues
1	Arg A:482	-	Pro A:483

(no "SAP(SNP)/Variant" information available for 3H8E)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOSOL_AP	PS00631	Cytosol aminopeptidase signature.	AMPA_PSEPU	347-354	2	A:347-354 B:347-354

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOSOL_AP	PS00631	Cytosol aminopeptidase signature.	AMPA_PSEPU	347-354	6	A:347-354 B:347-354

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOSOL_AP	PS00631	Cytosol aminopeptidase signature.	AMPA_PSEPU	347-354	2	A:347-354 B:347-354

(no "Exon" information available for 3H8E)

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:473
 aligned with AMPA_PSEPU | O86436 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:497
                                    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       490       
           AMPA_PSEPU     1 MELVVKSVAAASVKTATLVIPVGENRKLGAVAKAVDLASEGAISAVLKRGDLAGKPGQTLLLQNLQGLKAERVLLVGSGKDEALGDRTWRKLVASVAGVLKGLNGADAVLALDDVAVNNRDAHYGKYRLLAETLLDGEYVFDRFKSQKVEPRALKKVTLLADKAGQAEVERAVKHASAIATGMAFTRDLGNLPPNLCHPSFLAEQAKELGKAHKALKVEVLDEKKIKDLGMGAFYAVGQGSDQPPRLIVLNYQGGKKADKPFVLVGKGITFDTGGISLKPGAGMDEMKYDMCGAASVFGTLRAVLELQLPVNLVCLLACAENMPSGGATRPGDIVTTMSGQTVEILNTDAEGRLVLCDTLTYAERFKPQAVIDIATLTGACIVALGSHTTGLMGNNDDLVGQLLDAGKRADDRAWQLPLFDEYQEQLDSPFADMGNIGGPKAGTITAGCFLSRFAKAYNWAHMDIAGTAWISGGKDKGATGRPVPLLTQYLLDRAGA 497
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhh....eeeeee.hhh.hhhhhhhhhhh.hhhhhhhhh.........eeee..........eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhh.........---......eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhh......eeeeeeee........eeeeeee.---------------------hhhhhhhhhhhhhhhhhh...eeeeeeee.............eeee.....eeee.....hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eee...hhhhhhhhh.....ee......hhhhhhhhhhhh......eeeee.....ee......ee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOSOL_----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h8e A   1 MELVVKSVAAASVKTATLVIPVGENRKLGAVAKAVDLASEGAISAVLKRGDLAGKPGQTLLLQNLQGLKAERVLLVGSGKDEALGDRTWRKLVASVAGVLKGLNGADAVLALDDVAVNNRDAHYGKYRLLAETLLDGEYVFDRFKS---EPRALKKVTLLADKAGQAEVERAVKHASAIATGMAFTRDLGNLPPNLCHPSFLAEQAKELGKAHKALKVEVLDEKKIKDLGMGAFYAVGQGSDQPPRLIVLNYQGGKKADKPFVLVGKGI---------------------MCGAASVFGTLRAVLELQLPVNLVCLLACAENMPSGGATRPGDIVTTMSGQTVEILNTDAEGRLVLCDTLTYAERFKPQAVIDIATLTGACIVALGSHTTGLMGNNDDLVGQLLDAGKRADDRAWQLPLFDEYQEQLDSPFADMGNIGGPKAGTITAGCFLSRFAKAYNWAHMDIAGTAWISGGKDKGATGRPVPLLTQYLLDRAGA 497
                                    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        |-         -         -|      300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       
                                                                                                                                                                           146 150                                                                                                                    269                   291

Chain B from PDB  Type:PROTEIN  Length:473
 aligned with AMPA_PSEPU | O86436 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:497
                                    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       490       
           AMPA_PSEPU     1 MELVVKSVAAASVKTATLVIPVGENRKLGAVAKAVDLASEGAISAVLKRGDLAGKPGQTLLLQNLQGLKAERVLLVGSGKDEALGDRTWRKLVASVAGVLKGLNGADAVLALDDVAVNNRDAHYGKYRLLAETLLDGEYVFDRFKSQKVEPRALKKVTLLADKAGQAEVERAVKHASAIATGMAFTRDLGNLPPNLCHPSFLAEQAKELGKAHKALKVEVLDEKKIKDLGMGAFYAVGQGSDQPPRLIVLNYQGGKKADKPFVLVGKGITFDTGGISLKPGAGMDEMKYDMCGAASVFGTLRAVLELQLPVNLVCLLACAENMPSGGATRPGDIVTTMSGQTVEILNTDAEGRLVLCDTLTYAERFKPQAVIDIATLTGACIVALGSHTTGLMGNNDDLVGQLLDAGKRADDRAWQLPLFDEYQEQLDSPFADMGNIGGPKAGTITAGCFLSRFAKAYNWAHMDIAGTAWISGGKDKGATGRPVPLLTQYLLDRAGA 497
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhh....eeeeehhhhh.hhhhhhhhhhh.hhhhhhhhh.........eeee..........eeeee.......hhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhh........---......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhh......eeeeeeee........eeeeeee.---------------------hhhhhhhhhhhhhhhhhh...eeeeeeee.............eeee.....eeee.....hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eee...hhhhhhhhh.....ee......hhhhhhhhhhhh......eeeee.....ee......ee..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOSOL_----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h8e B   1 MELVVKSVAAASVKTATLVIPVGENRKLGAVAKAVDLASEGAISAVLKRGDLAGKPGQTLLLQNLQGLKAERVLLVGSGKDEALGDRTWRKLVASVAGVLKGLNGADAVLALDDVAVNNRDAHYGKYRLLAETLLDGEYVFDRFKS---EPRALKKVTLLADKAGQAEVERAVKHASAIATGMAFTRDLGNLPPNLCHPSFLAEQAKELGKAHKALKVEVLDEKKIKDLGMGAFYAVGQGSDQPPRLIVLNYQGGKKADKPFVLVGKGI---------------------MCGAASVFGTLRAVLELQLPVNLVCLLACAENMPSGGATRPGDIVTTMSGQTVEILNTDAEGRLVLCDTLTYAERFKPQAVIDIATLTGACIVALGSHTTGLMGNNDDLVGQLLDAGKRADDRAWQLPLFDEYQEQLDSPFADMGNIGGPKAGTITAGCFLSRFAKAYNWAHMDIAGTAWISGGKDKGATGRPVPLLTQYLLDRAGA 497
                                    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        |-         -         -|      300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       
                                                                                                                                                                           146 150                                                                                                                    269                   291

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 3H8E)

(no "CATH Domain" information available for 3H8E)

(no "Pfam Domain" information available for 3H8E)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AMPA_PSEPU | O86436)

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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3h8e)

	Sites
(no "Sites" information available for 3h8e)

	Cis Peptide Bonds
		Arg A:482 - Pro A:483	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3h8e
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	AMPA_PSEPU \| O86436
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	3.4.11.1
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		Disease Information	:	OMIM

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UniProtKB/Swiss-Prot
	AMPA_PSEPU \| O86436	:	3h8f 3h8g

1bll	X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH AMASTATIN: FORMULATION OF A CATALYTIC MECHANISM FEATURING A GEM-DIOLATE TRANSITION STATE
1gyt	X-RAY STRUCTURE OF AMINOPEPTIDASE A FROM ESCHERICHIA COLI AND A MODEL FOR THE NUCLEOPROTEIN COMPLEX IN XER SITE- SPECIFIC RECOMBINATION
3h8f	HIGH PH NATIVE STRUCTURE OF LEUCINE AMINOPEPTIDASE FROM PSEUDOMONAS PUTIDA
3h8g	BESTATIN COMPLEX STRUCTURE OF LEUCINE AMINOPEPTIDASE FROM PSEUDOMONAS PUTIDA

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (10, 10)

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