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Asym./Biol. Unit (Jmol Viewer)

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Title :   HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR

Authors :   E. A. Stura, V. Dive, L. Devel, B. Czarny, L. Vera, F. Beau

Date :   25 Jan 10 (Deposition) - 01 Sep 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Mmp12 Elastase Non-Chelating Inhibitor, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Devel, S. Garcia, B. Czarny, F. Beau, E. Lajeunesse, L. Vera, D. Georgiadis, E. Stura, V. Dive
Insights From Selective Non-Phosphinic Inhibitors Of Mmp-12 Tailored To Fit With An S1' Loop Canonical Conformation.
J. Biol. Chem. V. 285 35900 2010
PubMed-ID: 20817735 | Reference-DOI: 10.1074/JBC.M110.139634

Molecule 1 - MACROPHAGE METALLOELASTASE
	Chains	:	A
	EC Number	:	3.4.24.65
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET24A
	Fragment	:	MMP-12 CATALITIC SUBUNIT (RESIDUES 106-263)
	Gene	:	MMP12, HME
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MME, MATRIX METALLOPROTEINASE-12, MMP-12, MACROPHAGE ELASTASE, ME, HME

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	EEC	1	Ligand/Ion	N-[3-(3-PHENYLISOXAZOL-5-YL)PROPANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMYL-AMIDE
3	GLY	1	Mod. Amino Acid	GLYCINE
4	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:2 , HIS A:218 , HIS A:222 , HIS A:228	BINDING SITE FOR RESIDUE ZN A 264
2	AC2	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	BINDING SITE FOR RESIDUE ZN A 265
3	AC3	SOFTWARE	HOH A:17 , HOH A:24 , ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194	BINDING SITE FOR RESIDUE CA A 266
4	AC4	SOFTWARE	HOH A:25 , HOH A:36 , ASP A:124 , GLU A:199 , GLU A:201	BINDING SITE FOR RESIDUE CA A 267
5	AC5	SOFTWARE	ASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201	BINDING SITE FOR RESIDUE CA A 268
6	AC6	SOFTWARE	GLY A:2 , HOH A:22 , HOH A:65 , HOH A:85 , HOH A:95 , HOH A:103 , THR A:154 , GLY A:155 , GLY A:178 , GLY A:179 , LEU A:181 , ALA A:182 , THR A:215 , HIS A:218 , GLU A:219 , PRO A:232 , ALA A:234 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , LYS A:241 , HOH A:310	BINDING SITE FOR RESIDUE EEC A 1
7	AC7	SOFTWARE	EEC A:1 , ALA A:182 , HIS A:183 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , ZN A:264 , HOH A:269 , HOH A:272 , HOH A:355	BINDING SITE FOR RESIDUE GLY A 2

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:262	-	Gly A:263

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP12_HUMAN	215-224	1	A:215-224
2	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP12_HUMAN	279-328 329-375 377-425 426-470	1	A:2-2 - - -

(no "Exon" information available for 3LIR)

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:160
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:191
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294 
          MMP12_HUMAN   105 GGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGDPKENQRLPNPDNSEPALCDPNLSFDAVTTVG 295
               SCOP domains d3lira_ A: Macrophage elastase (MMP-12)                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Peptidase_M10-3lirA01 A:108-263                                                                                                                             -------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhh.-------------------------------. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------HEMOPEXIN_2       PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lir A 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG-------------------------------G   2
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        |-         -         -         -|
                                                                                                                                                                                        263                               2

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: Matrix metalloproteases, catalytic domain (199)

Protein domain: Macrophage elastase (MMP-12) (34)

Human (Homo sapiens) [TaxId: 9606] (34)

d3lira_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

Peptidase_M10-3lirA01

A:108-263

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MMP12_HUMAN | P39900)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds 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: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.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0050679	positive regulation of epithelial cell proliferation	Any process that activates or increases the rate or extent of epithelial cell proliferation.
	GO:0060054	positive regulation of epithelial cell proliferation involved in wound healing	Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0014070	response to organic cyclic compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
	GO:0035313	wound healing, spreading of epidermal cells	The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Tyr A:262 - Gly A:263	[ RasMol ]

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3lik	HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR
3lil	HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR
3ljg	HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (21, 21)

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