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Title :   STRUCTURE OF FULL-LENGTH PORCINE SYNOVIAL COLLAGENASE (MMP1) REVEALS A C-TERMINAL DOMAIN CONTAINING A CALCIUM-LINKED, FOUR-BLADED BETA-PROPELLER

Authors :   J. Li, P. Brick, D. M. Blow

Date :   24 Apr 95 (Deposition) - 29 Jan 96 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   J. Li, P. Brick, M. C. O'Hare, T. Skarzynski, L. F. Lloyd, V. A. Curry, I. M. Clark, H. F. Bigg, B. L. Hazleman, T. E. Cawston, D. M. Blow
Structure Of Full-Length Porcine Synovial Collagenase Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta-Propeller.
Structure V. 3 541 1995
PubMed-ID: 8590015 | Reference-DOI: 10.1016/S0969-2126(01)00188-5
(for further references see the PDB file header)

Molecule 1 - FIBROBLAST (INTERSTITIAL) COLLAGENASE (MMP-1)
	Chains	:	A
	EC Number	:	3.4.24.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	HTA	1	Ligand/Ion	N-[3-(N'-HYDROXYCARBOXAMIDO)-2-(2-METHYLPROPYL)-PROPANOYL]-O-TYROSINE-N-METHYLAMIDE
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HTA	2	Ligand/Ion	N-[3-(N'-HYDROXYCARBOXAMIDO)-2-(2-METHYLPROPYL)-PROPANOYL]-O-TYROSINE-N-METHYLAMIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201	BINDING SITE FOR RESIDUE CA A 993
2	AC2	SOFTWARE	ASP A:285 , GLN A:329 , ASP A:378 , ASP A:427	BINDING SITE FOR RESIDUE CA A 994
3	AC3	SOFTWARE	ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:834 , HOH A:837	BINDING SITE FOR RESIDUE CA A 995
4	AC4	SOFTWARE	ASP A:175 , GLY A:176 , GLY A:178 , ASN A:180 , ASP A:198 , GLU A:201	BINDING SITE FOR RESIDUE CA A 996
5	AC5	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	BINDING SITE FOR RESIDUE ZN A 997
6	AC6	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , HTA A:900	BINDING SITE FOR RESIDUE ZN A 998
7	AC7	SOFTWARE	GLY A:179 , ASN A:180 , LEU A:181 , ALA A:182 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , PRO A:238 , ASN A:239 , TYR A:240 , HOH A:505 , HOH A:531 , HOH A:559 , ZN A:998	BINDING SITE FOR RESIDUE HTA A 900

Asymmetric Unit

No.	Residues
1	A:278	-	A:466

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_PIG	215-224	1	A:215-224
2	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP1_PIG	275-324 325-371 374-422 423-466	4	A:275-324 A:325-371 A:374-422 A:423-466
3	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP1_PIG	317-332	1	A:317-332

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_PIG	215-224	2	A:215-224
2	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP1_PIG	275-324 325-371 374-422 423-466	8	A:275-324 A:325-371 A:374-422 A:423-466
3	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP1_PIG	317-332	2	A:317-332

(no "Exon" information available for 1FBL)

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
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Chain A from PDB  Type:PROTEIN  Length:367
 aligned with MMP1_PIG | P21692 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:367
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       
             MMP1_PIG   100 FVLTPGNPRWENTHLTYRIENYTPDLSREDVDRAIEKAFQLWSNVSPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTKNFRDYNLYRVAAHELGHSLGLSHSTDIGALMYPNYIYTGDVQLSQDDIDGIQAIYGPSENPVQPSGPQTPQVCDSKLTFDAITTLRGELMFFKDRFYMRTNSFYPEVELNFISVFWPQVPNGLQAAYEIADRDEVRFFKGNKYWAVRGQDVLYGYPKDIHRSFGFPSTVKNIDAAVFEEDTGKTYFFVAHECWRYDEYKQSMDTGYPKMIAEEFPGIGNKVDAVFQKDGFLYFFHGTRQYQFDFKTKRILTLQKANSWFNC 466
               SCOP domains d1fbla2 A:100-271 Fibroblast collagenase (MMP-1)                                                                                                                            d1fbla1 A:272-466 Collagenase (MMP1), C-terminal domain                                                                                                                                             SCOP domains
               CATH domains 1fblA01 A:100-273 Collagenase (Catalytic Domain)                                                                                                                              -1fblA02 A:275-465 Hemopexin                                                                                                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee........hhhhhhhhhhhhhhhhhh...eeeee......eeeeee.................eee..........eeee.............hhhhhhhhhhhh..........................hhhhhhhhhhh.........................eeeee..eeeeee..eeeee.......eeeehhhh.........eeeee....eeeeee..eeeee............hhhhh..........eeeee....eeeeee..eeeeee.............hhhh.........eeeee..eeeeee..eeeeee....eeeeeee..hhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------HEMOPEXIN_2  PDB: A:275-324 UniProt: 275-324      HEMOPEXIN_2  PDB: A:325-371 UniProt: 325-371   --HEMOPEXIN_2  PDB: A:374-422 UniProt: 374-422     HEMOPEXIN_2  PDB: A:423-466 UniProt: 423-466 PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       -------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fbl A 100 FVLTPGNPRWENTHLTYRIENYTPDLSREDVDRAIEKAFQLWSNVSPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTKNFRDYNLYRVAAHELGHSLGLSHSTDIGALMYPNYIYTGDVQLSQDDIDGIQAIYGPSENPVQPSGPQTPQVCDSKLTFDAITTLRGELMFFKDRFYMRTNSFYPEVELNFISVFWPQVPNGLQAAYEIADRDEVRFFKGNKYWAVRGQDVLYGYPKDIHRSFGFPSTVKNIDAAVFEEDTGKTYFFVAHECWRYDEYKQSMDTGYPKMIAEEFPGIGNKVDAVFQKDGFLYFFHGTRQYQFDFKTKRILTLQKANSWFNC 466
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459

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(

)

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)

Pig (Sus scrofa) (1)

1fblA01

A:100-273

Class: Mainly Beta (13760)

Architecture: 4 Propellor (14)

Topology: Hemopexin (14)

Homologous Superfamily: Hemopexin (14)

Pig (Sus scrofa) (1)

1fblA02

A:275-465

(no "Pfam Domain" information available for 1FBL)

Asymmetric Unit(hide GO term definitions)

Chain A (MMP1_PIG | P21692)

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: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:0032461	positive regulation of protein oligomerization	Any process that activates or increases the frequency, rate or extent of protein oligomerization.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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