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Title :   PSEUDOMONAS AERUGINOSA ELASTASE WITH PHOSPHORAMIDON

Authors :   D. B. Mckay, M. T. Overgaard

Date :   01 Jun 08 (Deposition) - 07 Jul 09 (Release) - 14 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Zinc Metalloprotease, Enzyme, Phosphoramidon, Protease Inhibitor Complex, Calcium, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zinc, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. T. Overgaard, D. B. Mckay
Structure Of The Elastase Of Pseudomonas Aeruginosa Complexed With Phosphoramidon
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ELASTASE
	Chains	:	A
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	ISOLATED AS MATURE EXTRACELLULAR PROTEASE FROM PSEUDOMONAS AERUGINOSA CULTURES
	Synonym	:	PSEUDOLYSIN; NEUTRAL METALLOPROTEINASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	RDF	1	Ligand/Ion	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
3	SO4	3	Ligand/Ion	SULFATE ION
4	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:140 , HIS A:144 , GLU A:164 , RDF A:2001	BINDING SITE FOR RESIDUE ZN A 302
2	AC2	SOFTWARE	ASP A:136 , GLU A:172 , GLU A:175 , ASP A:183 , LEU A:185 , HOH A:3058	BINDING SITE FOR RESIDUE CA A 303
3	AC3	SOFTWARE	LYS A:11 , TYR A:188 , GLY A:193 , SER A:194 , GLY A:195 , TYR A:258 , ARG A:274 , HOH A:3296	BINDING SITE FOR RESIDUE SO4 A 401
4	AC4	SOFTWARE	ARG A:29 , GLN A:65 , ASN A:67 , GLY A:68 , HOH A:3331	BINDING SITE FOR RESIDUE SO4 A 402
5	AC5	SOFTWARE	LYS A:85 , ARG A:88 , HOH A:3055	BINDING SITE FOR RESIDUE SO4 A 403
6	AC6	SOFTWARE	GLU A:111 , ASN A:112 , ALA A:113 , TYR A:114 , MET A:128 , PHE A:129 , LEU A:132 , HIS A:140 , GLU A:141 , HIS A:144 , TYR A:155 , GLU A:164 , LEU A:197 , ARG A:198 , ASN A:212 , HIS A:223 , ARG A:231 , ARG A:288 , SER A:291 , THR A:292 , ZN A:302 , HOH A:3003 , HOH A:3034 , HOH A:3075 , HOH A:3209 , HOH A:3210	BINDING SITE FOR RESIDUE RDF A 2001

Asymmetric/Biological Unit

No.	Residues
1	A:30	-	A:58
2	A:270	-	A:297

Asymmetric/Biological Unit

No.	Residues
1	Cys A:58	-	Pro A:59
2	Tyr A:63	-	Lys A:64

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ELAS_PSEAE_004 *	K	211	I	ELAS_PSEAE	---	---	A	K	14	I
2	UniProt	VAR_ELAS_PSEAE_005 *	S	241	G	ELAS_PSEAE	---	---	A	S	44	G
3	UniProt	VAR_ELAS_PSEAE_006 *	K	282	D	ELAS_PSEAE	---	---	A	K	85	D
4	UniProt	VAR_ELAS_PSEAE_007 *	M	325	V	ELAS_PSEAE	---	---	A	M	128	V
5	UniProt	VAR_ELAS_PSEAE_008 *	R	471	S	ELAS_PSEAE	---	---	A	R	274	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	ELAS_PSEAE	334-343	1	A:137-146

(no "Exon" information available for 3DBK)

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:298
 aligned with ELAS_PSEAE | P14756 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:298
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487        
           ELAS_PSEAE   198 AEAGGPGGNQKIGKYTYGSDYGPLIVNDRCEMDDGNVITVDMNSSTDDSKTTPFRFACPTNTYKQVNGAYSPLNDAHFFGGVVFKLYRDWFGTSPLTHKLYMKVHYGRSVENAYWDGTAMLFGDGATMFYPLVSLDVAAHEVSHGFTEQNSGLIYRGQSGGMNEAFSDMAGEAAEFYMRGKNDFLIGYDIKKGSGALRYMDQPSRDGRSIDNASQYYNGIDVHHSSGVYNRAFYLLANSPGWDTRKAFEVFVDANRYYWTATSNYNSGACGVIRSAQNRNYSAADVTRAFSTVGVTCP 495
               SCOP domains d3dbka_ A: Elastase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3dbkA01 A:1-152  [code=3.10.170.10, no name defined]                                                                                                    3dbkA02 A:153-298 Neutral Protease Domain 2                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eeeee...eeeee......ee...........eeeee.............................hhhhhhhhhhhhhhhhhhhhhh.......eeeee........eee....eee...........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....eehhhhh......ee..hhhhhh....hhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------I-----------------------------G----------------------------------------D------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------------S------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbk A   1 AEAGGPGGNQKIGKYTYGSDYGPLIVNDRCEMDDGNVITVDMNSSTDDSKTTPFRFACPTNTYKQVNGAYSPLNDAHFFGGVVFKLYRDWFGTSPLTHKLYMKVHYGRSVENAYWDGTAMLFGDGATMFYPLVSLDVAAHEVSHGFTEQNSGLIYRGQSGGMNEAFSDMAGEAAEFYMRGKNDFLIGYDIKKGSGALRYMDQPSRDGRSIDNASQYYNGIDVHHSSGVYNRAFYLLANSPGWDTRKAFEVFVDANRYYWTATSNYNSGACGVIRSAQNRNYSAADVTRAFSTVGVTCP 298
                                    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

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: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Thermolysin-like (130)

Protein domain: Elastase (3)

Pseudomonas aeruginosa [TaxId: 287] (3)

d3dbka_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Elastase; domain 1 (68)

Homologous Superfamily: [code=3.10.170.10, no name defined] (67)

Pseudomonas aeruginosa. Organism_taxid: 287. (2)

3dbkA01

A:1-152

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Neutral Protease; domain 2 (68)

Homologous Superfamily: Neutral Protease Domain 2 (68)

Pseudomonas aeruginosa. Organism_taxid: 287. (2)

3dbkA02

A:153-298

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ELAS_PSEAE | P14756)

molecular function
	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:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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: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.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Cys A:58 - Pro A:59	[ RasMol ]
		Tyr A:63 - Lys A:64	[ RasMol ]

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	ELAS_PSEAE \| P14756	:	1ezm 1u4g

1ezm	PSEUDOMONAS AERUGINOSA ELASTASE NATIVE STRUCTURE 1.5 A RESOLUTION
1u4g	ELASTASE OF PSEUDOMONAS AERUGINOSA WITH AN INHIBITOR

Description

Compounds

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Ligands, Modified Residues, Ions (4, 6)

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SS Bonds (2, 2)

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