DB code: S00395

RLCP classification	1.13.13000.460 : Hydrolysis
CATH domain	3.40.390.10 : Collagenase (Catalytic Domain)	Catalytic domain
E.C.	3.4.24.23
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.40.390.10 : Collagenase (Catalytic Domain)	S00394 S00397 S00398 S00399 D00232 D00236 M00101

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	MEROPS	Pfam
P09237	Matrilysin	EC 3.4.24.23 Pump-1 protease Uterine metalloproteinase Matrix metalloproteinase-7 MMP-7 Matrin	NP_002414.1 (Protein) NM_002423.3 (DNA/RNA sequence)	M10.008 (Metallo)	PF00413 (Peptidase_M10) PF01471 (PG_binding_1) [Graphical View]

KEGG enzyme name
matrilysin matrin uterine metalloendopeptidase matrix metalloproteinase 7 putative (or punctuated) metalloproteinase-1 matrix metalloproteinase pump 1 MMP 7 PUMP-1 proteinase PUMP metalloproteinase pump-1 putative metalloproteinase MMP

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P09237	MMP7_HUMAN	Cleavage of 14-Ala-\|-Leu-15 and 16-Tyr-\|-Leu- 17 in B chain of insulin. No action on collagen types I, II, IV, V. Cleaves gelatin chain alpha-2(I) > alpha-1(I).		Secreted, extracellular space, extracellular matrix (Probable).	Binds 2 calcium ions per subunit. Binds 2 zinc ions per subunit.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Cofactors		Substrates				Products		Intermediates
KEGG-id	C00076	C00038	C03397	C03396	C00001	C01406	C00017	C00012
E.C.
Compound	Calcium	Zinc	Gelatin chain alpha2(I)	Gelatin chain alpha1(I)	H2O	Azocoll	Protein	Peptide
Type	divalent metal (Ca2+, Mg2+)	heavy metal	peptide/protein	peptide/protein	H2O	peptide/protein	peptide/protein	peptide/protein
ChEBI	29108 29108	29105 29105			15377 15377
PubChem	271 271	32051 32051			22247451 962 22247451 962

1mmpA	Bound:2x_CA	Bound:2x_ZN	Unbound	Unbound		Unbound	Bound:RSS	Unbound	Unbound
1mmpB	Bound:2x_CA	Bound:2x_ZN	Unbound	Unbound		Unbound	Bound:RSS	Unbound	Unbound
1mmqA	Bound:2x_CA	Bound:2x_ZN	Unbound	Unbound		Unbound	Unbound	Unbound	Intermediate-analogue:RRS
1mmrA	Bound:2x_CA	Bound:2x_ZN	Unbound	Unbound		Unbound	Unbound	Unbound	Transition-state-analogue:SRS

Reference for Active-site residues
resource	references	E.C.
Swiss-prot;P09237

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1mmpA	GLU 219	HIS 218;HIS 222;HIS 228(Zinc binding)
1mmpB	GLU 219	HIS 218;HIS 222;HIS 228(Zinc binding)
1mmqA	GLU 219	HIS 218;HIS 222;HIS 228(Zinc binding)
1mmrA	GLU 219	HIS 218;HIS 222;HIS 228(Zinc binding)

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	p.6608-6609, Fig.5	2
[4]	p.15835-15838
[8]	p.16022-16023

References
[1]
Resource
Comments	X-ray crystallography (1.9-2.4 Angstroms)
Medline ID	95275856
PubMed ID	7756291
Journal	Biochemistry
Year	1995
Volume	34
Pages	6602-10
Authors	Browner MF, Smith WW, Castelhano AL
Title	Matrilysin-inhibitor complexes: common themes among metalloproteases.
Related PDB	1mmp 1mmq 1mmr
Related UniProtKB	P09237
[2]
Resource
Comments
Medline ID
PubMed ID	8729000
Journal	Int J Biochem Cell Biol
Year	1996
Volume	28
Pages	123-36
Authors	Wilson CL, Matrisian LM
Title	Matrilysin: an epithelial matrix metalloproteinase with potentially novel functions.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	8626782
Journal	J Biol Chem
Year	1996
Volume	271
Pages	4335-41
Authors	Shipley JM, Doyle GA, Fliszar CJ, Ye QZ, Johnson LL, Shapiro SD, Welgus HG, Senior RM
Title	The structural basis for the elastolytic activity of the 92-kDa and 72-kDa gelatinases. Role of the fibronectin type II-like repeats.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	8961947
Journal	Biochemistry
Year	1996
Volume	35
Pages	15831-8
Authors	Cha J, Pedersen MV, Auld DS
Title	Metal and pH dependence of heptapeptide catalysis by human matrilysin.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	9101722
Journal	Biochim Biophys Acta
Year	1997
Volume	1334
Pages	261-72
Authors	Windsor LJ, Steele DL, LeBlanc SB, Taylor KB
Title	Catalytic domain comparisons of human fibroblast-type collagenase, stromelysin-1, and matrilysin.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	9218437
Journal	J Biol Chem
Year	1997
Volume	272
Pages	18071-6
Authors	Mecham RP, Broekelmann TJ, Fliszar CJ, Shapiro SD, Welgus HG, Senior RM
Title	Elastin degradation by matrix metalloproteinases. Cleavage site specificity and mechanisms of elastolysis.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	10187841
Journal	J Biol Chem
Year	1999
Volume	274
Pages	10497-504
Authors	Higashi S, Miyazaki K
Title	Reactive site-modified tissue inhibitor of metalloproteinases-2 inhibits the cell-mediated activation of progelatinase A.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	9398337
Journal	Biochemistry
Year	1997
Volume	36
Pages	16019-24
Authors	Cha J, Auld DS
Title	Site-directed mutagenesis of the active site glutamate in human matrilysin: investigation of its role in catalysis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID	9737711
Journal	FASEB J
Year	1998
Volume	12
Pages	1075-95
Authors	Massova I, Kotra LP, Fridman R, Mobashery S
Title	Matrix metalloproteinases: structures, evolution, and diversification.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID	11389678
Journal	Biochem J
Year	2001
Volume	356
Pages	705-18
Authors	Marchenko GN, Ratnikov BI, Rozanov DV, Godzik A, Deryugina EI, Strongin AY
Title	Characterization of matrix metalloproteinase-26, a novel metalloproteinase widely expressed in cancer cells of epithelial origin.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	11686860
Journal	Respir Res
Year	2001
Volume	2
Pages	10-9
Authors	Parks WC, Shapiro SD
Title	Matrix metalloproteinases in lung biology.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID	11790786
Journal	J Biol Chem
Year	2002
Volume	277
Pages	11201-7
Authors	Bernardo MM, Brown S, Li ZH, Fridman R, Mobashery S
Title	Design, synthesis, and characterization of potent, slow-binding inhibitors that are selective for gelatinases.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID	12051944
Journal	J Mol Biol
Year	2002
Volume	319
Pages	173-81
Authors	Rowsell S, Hawtin P, Minshull CA, Jepson H, Brockbank SM, Barratt DG, Slater AM, McPheat WL, Waterson D, Henney AM, Pauptit RA
Title	Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID	12119297
Journal	J Biol Chem
Year	2002
Volume	277
Pages	35168-75
Authors	Park HI, Turk BE, Gerkema FE, Cantley LC, Sang QX
Title	Peptide substrate specificities and protein cleavage sites of human endometase/matrilysin-2/matrix metalloproteinase-26.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID	12759346
Journal	J Biol Chem
Year	2003
Volume	278
Pages	28403-9
Authors	Fu X, Kassim SY, Parks WC, Heinecke JW
Title	Hypochlorous acid generated by myeloperoxidase modifies adjacent tryptophan and glycine residues in the catalytic domain of matrix metalloproteinase-7 (matrilysin): an oxidative mechanism for restraining proteolytic activity during inflammation.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID	12801907
Journal	J Biochem (Tokyo)
Year	2003
Volume	133
Pages	571-6
Authors	Oneda H, Shiihara M, Inouye K
Title	Inhibitory effects of green tea catechins on the activity of human matrix metalloproteinase 7 (matrilysin).
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the peptidase family-M10A. Moreover, this enzyme belongs to Matrix metalloproteinases (MMP-7). According to the paper [1], the catalytic mechanism was proposed as follows: (1) The catalytic water, which interacts with both Glu219 and the catalytic zinc, would attack on the carbonyl group as a nucleophile, forming the tetrahedral intermediate. (2) Another protein-bound water would form a hydrogen bond with the oxyanion of the tetrahedral intermediate. The paper [4] described the lower pKa and higher pKa in the catalysis. This paper mentioned that the lower pKa was ascribed to the glutamate residue (corresponding to Glu219) interacting with zinc-bound water, that is suggested to act as a proton-accepting group (or a general base) for one proton from the zinc-coordinated water molecule in catalysis, whilst the higher pKa was ascribed to a zinc-bound water or tyrosine residue in the active site (Tyr237 or Tyr240) as a proton donor (or a general acid). (However, the sidechains of Tyr237 and Tyr240 are oriented away from the active site, suggesting that they are not involved in catalysis.) In contrast, the literature [8] proposed a different function of the catalytic glutamate, Glu219, from that suggested in the above papers [1] & [4]. This paper [8] suggested that the pKa of Glu219 must be abnormally high and the sidechain of the residue must be protonated, due to its hydrophobic environment. Thus, this paper suggested that the hydrolysis of peptides might occur by the direct nucleophilic attack of the ionized zinc hydroxide on the carbonyl group to form a tetrahedral intermediate, whilst Glu219 assists the zinc in stabilizing the transition state or acts as a general acid by donating a proton to the leaving amine as the metal-bound tetrahedral intermediate collapses to products in the next step. The active site structures with transition-sate analogue (PDB;1mmr) supports this mechanism. Taken together, the catalytic reaction proceeds as follows: (1) The catalytic water, which interacts with both Glu219 and the catalytic zinc, would attack on the carbonyl group as a nucleophile, forming the tetrahedral intermediate. (2) The tetrahedral intermediate is stabilized by Glu219 and the catalytic zinc ion. (3) Glu219 acts as a general acid to protonate the leaving amine group, when the intermediate collapses to products.

Comments

This enzyme belongs to the peptidase family-M10A. Moreover, this enzyme belongs to Matrix metalloproteinases (MMP-7).
According to the paper [1], the catalytic mechanism was proposed as follows:
(1) The catalytic water, which interacts with both Glu219 and the catalytic zinc, would attack on the carbonyl group as a nucleophile, forming the tetrahedral intermediate.
(2) Another protein-bound water would form a hydrogen bond with the oxyanion of the tetrahedral intermediate.
The paper [4] described the lower pKa and higher pKa in the catalysis. This paper mentioned that the lower pKa was ascribed to the glutamate residue (corresponding to Glu219) interacting with zinc-bound water, that is suggested to act as a proton-accepting group (or a general base) for one proton from the zinc-coordinated water molecule in catalysis, whilst the higher pKa was ascribed to a zinc-bound water or tyrosine residue in the active site (Tyr237 or Tyr240) as a proton donor (or a general acid). (However, the sidechains of Tyr237 and Tyr240 are oriented away from the active site, suggesting that they are not involved in catalysis.)
In contrast, the literature [8] proposed a different function of the catalytic glutamate, Glu219, from that suggested in the above papers [1] & [4]. This paper [8] suggested that the pKa of Glu219 must be abnormally high and the sidechain of the residue must be protonated, due to its hydrophobic environment.
Thus, this paper suggested that the hydrolysis of peptides might occur by the direct nucleophilic attack of the ionized zinc hydroxide on the carbonyl group to form a tetrahedral intermediate, whilst Glu219 assists the zinc in stabilizing the transition state or acts as a general acid by donating a proton to the leaving amine as the metal-bound tetrahedral intermediate collapses to products in the next step. The active site structures with transition-sate analogue (PDB;1mmr) supports this mechanism.
Taken together, the catalytic reaction proceeds as follows:
(1) The catalytic water, which interacts with both Glu219 and the catalytic zinc, would attack on the carbonyl group as a nucleophile, forming the tetrahedral intermediate.
(2) The tetrahedral intermediate is stabilized by Glu219 and the catalytic zinc ion.
(3) Glu219 acts as a general acid to protonate the leaving amine group, when the intermediate collapses to products.

Created	Updated
2002-08-27	2009-02-26