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Title :   CRYSTAL STRUCTURE ANALYSIS OF HUMAN MACROPHAGE ELASTASE MMP-12

Authors :   H. Nar, K. Werle, M. M. T. Bauer, H. Dollinger, B. Jung

Date :   03 Jul 01 (Deposition) - 03 Jul 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Matrix Metalloproteinase, Mmp-12, Chronic Obstructive Pulmonary Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Nar, K. Werle, M. M. Bauer, H. Dollinger, B. Jung
Crystal Structure Of Human Macrophage Elastase (Mmp-12) In Complex With A Hydroxamic Acid Inhibitor.
J. Mol. Biol. V. 312 743 2001
PubMed-ID: 11575929 | Reference-DOI: 10.1006/JMBI.2001.4953
(for further references see the PDB file header)

Molecule 1 - MACROPHAGE ELASTASE MMP-12
	Chains	:	A, B
	EC Number	:	3.4.24.65
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MACROPHAGE METALLOELASTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	CGS	2	Ligand/Ion	N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CGS	1	Ligand/Ion	N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CGS	1	Ligand/Ion	N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:119 , HIS A:123 , HIS A:129 , CGS A:998	BINDING SITE FOR RESIDUE ZN A 257
02	AC2	SOFTWARE	HIS A:69 , ASP A:71 , HIS A:84 , HIS A:97	BINDING SITE FOR RESIDUE ZN A 258
03	AC3	SOFTWARE	ASP A:76 , GLY A:77 , GLY A:79 , ILE A:81 , ASP A:99 , GLU A:102	BINDING SITE FOR RESIDUE CA A 259
04	AC4	SOFTWARE	ASP A:59 , GLY A:91 , GLY A:93 , ASP A:95 , HOH A:555 , HOH A:857	BINDING SITE FOR RESIDUE CA A 260
05	AC5	SOFTWARE	ASP A:25 , GLU A:100 , GLU A:102 , HOH A:722	BINDING SITE FOR RESIDUE CA A 261
06	AC6	SOFTWARE	HIS B:119 , HIS B:123 , HIS B:129 , CGS B:999	BINDING SITE FOR RESIDUE ZN B 257
07	AC7	SOFTWARE	HIS B:69 , ASP B:71 , HIS B:84 , HIS B:97	BINDING SITE FOR RESIDUE ZN B 258
08	AC8	SOFTWARE	ASP B:76 , GLY B:77 , GLY B:79 , ILE B:81 , ASP B:99 , GLU B:102	BINDING SITE FOR RESIDUE CA B 259
09	AC9	SOFTWARE	ASP B:59 , GLY B:91 , GLY B:93 , ASP B:95 , HOH B:572 , HOH B:863	BINDING SITE FOR RESIDUE CA B 260
10	BC1	SOFTWARE	ASP B:25 , GLU B:100 , GLU B:102 , HOH B:851	BINDING SITE FOR RESIDUE CA B 261
11	BC2	SOFTWARE	GLY A:80 , ILE A:81 , LEU A:82 , ALA A:83 , THR A:116 , HIS A:119 , GLU A:120 , HIS A:123 , HIS A:129 , PRO A:139 , ZN A:257 , HOH A:603	BINDING SITE FOR RESIDUE CGS A 998
12	BC3	SOFTWARE	GLY B:80 , ILE B:81 , LEU B:82 , ALA B:83 , THR B:116 , HIS B:119 , GLU B:120 , HIS B:123 , HIS B:129 , PRO B:139 , ZN B:257 , HOH B:730	BINDING SITE FOR RESIDUE CGS B 999

(no "SS Bond" information available for 1JIZ)

(no "Cis Peptide Bond" information available for 1JIZ)

(no "SAP(SNP)/Variant" information available for 1JIZ)

Asymmetric Unit (1, 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	2	A:116-125 B:116-125

Biological Unit 1 (1, 1)

	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:116-125 -

Biological Unit 2 (1, 1)

	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	- B:116-125

(no "Exon" information available for 1JIZ)

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:166
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:166
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          MMP12_HUMAN    99 HFREMPGGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 264
               SCOP domains d1jiza_ A: Macrophage elastase (MMP-12)                                                                                                                                SCOP domains
               CATH domains 1jizA00 A:-1-165 Collagenase (Catalytic Domain)                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jiz A  -1 GFREMPGGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 165
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159      
                            ||                                                                                                                                                                    
                           -1|                                                                                                                                                                    
                             1

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:166
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          MMP12_HUMAN    99 HFREMPGGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 264
               SCOP domains d1jizb_ B: Macrophage elastase (MMP-12)                                                                                                                                SCOP domains
               CATH domains 1jizB00 B:-1-165 Collagenase (Catalytic Domain)                                                                                                                        CATH domains
           Pfam domains (1) ---------Peptidase_M10-1jizB01 B:9-164                                                                                                                               - Pfam domains (1)
           Pfam domains (2) ---------Peptidase_M10-1jizB02 B:9-164                                                                                                                               - Pfam domains (2)
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jiz B  -1 GFREMPGGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 165
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159      
                           -1|                                                                                                                                                                    
                             1

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	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) (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)

1a	d1jiza_	A:
1b	d1jizb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Human (Homo sapiens) (153)

1a	1jizA00	A:-1-165
1b	1jizB00	B:-1-165

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

1a	Peptidase_M10-1jizB01	B:9-164
1b	Peptidase_M10-1jizB02	B:9-164

Asymmetric Unit(hide GO term definitions)

Chain A,B (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 Unit
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Description

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Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

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