3NH5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF E177A-MUTANT MURINE AMINOACYLASE 3

Authors :   J. M. Hsieh, K. Tsirulnikov, M. R. Sawaya, N. Magilnick, N. Abuladze, I. J. Abramson, A. Pushkin

Date :   14 Jun 10 (Deposition) - 20 Oct 10 (Release) - 03 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

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

Reference :   J. M. Hsieh, K. Tsirulnikov, M. R. Sawaya, N. Magilnick, N. Abuladze, I. Kurtz, J. Abramson, A. Pushkin
Structures Of Aminoacylase 3 In Complex With Acetylated Substrates.
Proc. Natl. Acad. Sci. Usa V. 107 17962 2010
PubMed-ID: 20921362 | Reference-DOI: 10.1073/PNAS.1006687107

Molecule 1 - ASPARTOACYLASE-2
	Chains	:	A
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ACY-3, ACY3, ASPA2
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	AMINOACYLASE-3, ACY-3, AMINOACYLASE III, ACYLASE III, HEPATITIS C VIRUS CORE-BINDING PROTEIN 1, HCBP1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	FMT	1	Ligand/Ion	FORMIC ACID
4	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FMT	2	Ligand/Ion	FORMIC ACID
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:21 , GLU A:24 , HIS A:116 , ACT A:322	BINDING SITE FOR RESIDUE ZN A 319
2	AC2	SOFTWARE	HIS A:137 , HIS A:140	BINDING SITE FOR RESIDUE CL A 320
3	AC3	SOFTWARE	ALA A:120 , ASN A:121 , GLN A:247 , ASP A:248 , ASP A:250 , ILE A:282	BINDING SITE FOR RESIDUE CL A 321
4	AC4	SOFTWARE	HIS A:21 , GLU A:24 , ARG A:63 , HIS A:116 , ASN A:117 , GLU A:284 , TYR A:287 , ZN A:319 , FMT A:323	BINDING SITE FOR RESIDUE ACT A 322
5	AC5	SOFTWARE	HIS A:21 , ARG A:63 , ASN A:70 , ARG A:71 , TYR A:287 , ACT A:322	BINDING SITE FOR RESIDUE FMT A 323

(no "SS Bond" information available for 3NH5)

Asymmetric Unit

No.	Residues
1	Gly A:101	-	Pro A:102
2	Gly A:179	-	Pro A:180

(no "SAP(SNP)/Variant" information available for 3NH5)

(no "PROSITE Motif" information available for 3NH5)

(no "Exon" information available for 3NH5)

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:306
 aligned with ACY3_MOUSE | Q91XE4 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:306
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306      
           ACY3_MOUSE     7 SREPLLRVAVTGGTHGNEMCGVYLARYWLQNPGELQRPSFSAMPVLANPAATAACCRYLDRDLNRSCTLTFLGSTATPDDPYEVKRARELNQLLGPKGTGQAFDFTLDLHNTTANTGVCLISESNISFNLHLCHYLQRQNPGMPCRLFLYEPAGTETFSVESISKNGICLEMGPQPQGVLRADLFSRMRALVASILDFIELFNQGMDLPAFEMDIYRNLGSVDFPRTADGDLAGTVHPQLQDHDFEPLRPGEPIFKLFSGEDVLYEGDSIVYPVFINEAAYYEKHVAFLKSEKIRVTVPALLRLTP 312
               SCOP domains d3nh5a_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---AstE_AspA-3nh5A01 A:10-300                                                                                                                                                                                                                                                                         ------------ Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhh.......hhhhh.hhhhhhh......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee...hhhhhhhhhhhhhhh....eeeee..........hhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee...........eee................eeeee....eee.......eee...hhhhh.....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nh5 A   7 SREPLLRVAVTGGTHGNEMCGVYLARYWLQNPGELQRPSFSAMPVLANPAATAACCRYLDRDLNRSCTLTFLGSTATPDDPYEVKRARELNQLLGPKGTGQAFDFTLDLHNTTANTGVCLISESNISFNLHLCHYLQRQNPGMPCRLFLYEPAGTETFSVESISKNGICLAMGPQPQGVLRADLFSRMRALVASILDFIELFNQGMDLPAFEMDIYRNLGSVDFPRTADGDLAGTVHPQLQDHDFEPLRPGEPIFKLFSGEDVLYEGDSIVYPVFINEAAYYEKHVAFLKSEKIRVTVPALLRLTP 312
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Zn-dependent exopeptidases (214)

Family: automated matches (6)

Protein domain: automated matches (6)

Mouse (Mus musculus) [TaxId: 10090] (4)

d3nh5a_

(no "CATH Domain" information available for 3NH5)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MH (119)

Family: AstE_AspA (12)

Mus musculus (Mouse) (4)

AstE_AspA-3nh5A01

A:10-300

Asymmetric Unit(hide GO term definitions)

Chain A (ACY3_MOUSE | Q91XE4)

molecular function
	GO:0004046	aminoacylase activity	Catalysis of the reaction: an N-acyl-L-amino acid + H2O = a carboxylate + an L-amino acid.
	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:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:101 - Pro A:102	[ RasMol ]
		Gly A:179 - Pro A:180	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3nh5
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	ACY3_MOUSE \| Q91XE4
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	3.5.1.-
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	ACY3_MOUSE \| Q91XE4
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UniProtKB/Swiss-Prot
	ACY3_MOUSE \| Q91XE4	:	3nfz 3nh4 3nh8

3nfz	THE SAME PROTEIN IN COMPLEX WITH N-ACETYL-L-TYROSINE.
3nh4	THE SAME PROTEIN, BUT WILD-TYPE IN COMPLEX WITH ACETATE AND FORMATE.
3nh8	THE SAME PROTEIN (E177A MUTATION) IN COMPLEX WITH N-ACETYL- S-1,2-DICHLOROVINYL-L-CYSTEINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

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