DB code: S00397

RLCP classification 1.13.13000.460 : Hydrolysis
CATH domain 3.40.390.10 : Collagenase (Catalytic Domain) Catalytic domain
E.C. 3.4.24.34
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.390.10 : Collagenase (Catalytic Domain) S00394 S00395 S00398 S00399 D00232 D00236 M00101

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq MEROPS Pfam
P22894 Neutrophil collagenase
Matrix metalloproteinase-8
MMP-8
PMNL collagenase
PMNL-CL
EC 3.4.24.34
NP_002415.1 (Protein)
NM_002424.2 (DNA/RNA sequence)
M10.002 (Metallo)
PF00045 (Hemopexin)
PF00413 (Peptidase_M10)
PF01471 (PG_binding_1)
[Graphical View]

KEGG enzyme name
neutrophil collagenase
matrix metalloproteinase 8
PMNL collagenase
MMP-8

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P22894 MMP8_HUMAN Cleavage of interstitial collagens in the triple helical domain. Unlike EC 3.4.24.7, this enzyme cleaves type III collagen more slowly than type I. Cytoplasmic granule. Secreted, extracellular space, extracellular matrix (Probable). Note=Stored in intracellular granules. Binds 3 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 C00211 C00001 C00017 C00012
E.C.
Compound Calcium Zinc Collagen H2O Protein Peptide
Type divalent metal (Ca2+, Mg2+) heavy metal amine group,carboxyl group,peptide/protein H2O peptide/protein peptide/protein
ChEBI 29108
29105
15377
PubChem 271
32051
22247451
962
1a85A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1a86A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1bzsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1i73A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Analogue:PRO-LEU-PAT Unbound
1i76A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Analogue:BSI Unbound
1janA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Analogue:PRO-LEU-GLY-HOA Unbound Unbound Unbound
1jaoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1japA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Analogue:PRO-LEU-GLY-HOA Unbound Unbound Unbound
1jaqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1kbcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1kbcB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1mmbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:2x_ZN Unbound Unbound Unbound Unbound
1mncA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:2x_ZN Unbound Unbound Unbound Intermediate-analogue:PLH

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1a85A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1a86A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1bzsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1i73A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1i76A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1janA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1jaoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1japA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1jaqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1kbcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1kbcB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1mmbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 198 HIS 197;HIS 201;HIS 207(Zinc binding)
1mncA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 219 HIS 218;HIS 222;HIS 228(Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.836-838, Fig.7, Fig.8
[15]
p.18663

References
[1]
Resource
Comments X-ray crystallography
Medline ID 94139930
PubMed ID 8307185
Journal FEBS Lett
Year 1994
Volume 338
Pages 227-33
Authors Reinemer P, Grams F, Huber R, Kleine T, Schnierer S, Piper M, Tschesche H, Bode W
Title Structural implications for the role of the N terminus in the 'superactivation' of collagenases. A crystallographic study.
Related PDB 1jan
Related UniProtKB P22894
[2]
Resource
Comments X-ray crystallography (2.1 Angstroms)
Medline ID 95384762
PubMed ID 7656015
Journal Nat Struct Biol
Year 1994
Volume 1
Pages 119-23
Authors Stams T, Spurlino JC, Smith DL, Wahl RC, Ho TF, Qoronfleh MW, Banks TM, Rubin B
Title Structure of human neutrophil collagenase reveals large S1' specificity pocket.
Related PDB 1mnc
Related UniProtKB P22894
[3]
Resource
Comments X-ray crystallography (2.0 Angstroms)
Medline ID 94185631
PubMed ID 8137810
Journal EMBO J
Year 1994
Volume 13
Pages 1263-9
Authors Bode W, Reinemer P, Huber R, Kleine T, Schnierer S, Tschesche H
Title The X-ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity.
Related PDB 1jap
Related UniProtKB P22894
[4]
Resource
Comments X-ray crystallography (2.4/2.25 Angstroms)
Medline ID
PubMed ID 7737183
Journal Eur J Biochem
Year 1995
Volume 228
Pages 830-41
Authors Grams F, Reinemer P, Powers JC, Kleine T, Pieper M, Tschesche H, Huber R, Bode W
Title X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design.
Related PDB 1jao 1jaq
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7663339
Journal Protein Sci
Year 1995
Volume 4
Pages 823-40
Authors Stocker W, Grams F, Baumann U, Reinemer P, Gomis-Ruth FX, McKay DB, Bode W
Title The metzincins--topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8590015
Journal Structure
Year 1995
Volume 3
Pages 541-9
Authors Li J, Brick P, O'Hare MC, Skarzynski T, Lloyd LF, Curry VA, Clark IM, Bigg HF, Hazleman BL, Cawston TE, et al
Title Structure of full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four-bladed beta-propeller.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-ray crystallography (2.1 Angstroms)
Medline ID
PubMed ID 7577999
Journal Biochemistry
Year 1995
Volume 34
Pages 14012-20
Authors Grams F, Crimmin M, Hinnes L, Huxley P, Pieper M, Tschesche H, Bode W
Title Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor.
Related PDB 1mmb
Related UniProtKB
[8]
Resource
Comments X-ray crystallography (1.8 Angstroms)
Medline ID 97390108
PubMed ID 9249047
Journal Eur J Biochem
Year 1997
Volume 247
Pages 356-63
Authors Betz M, Huxley P, Davies SJ, Mushtaq Y, Pieper M, Tschesche H, Bode W, Gomis-Ruth FX
Title 1.8-A crystal structure of the catalytic domain of human neutrophil collagenase (matrix metalloproteinase-8) complexed with a peptidomimetic hydroxamate primed-side inhibitor with a distinct selectivity profile.
Related PDB 1kbc
Related UniProtKB P22894
[9]
Resource
Comments X-ray crystallography
Medline ID 98318039
PubMed ID 9655333
Journal Protein Sci
Year 1998
Volume 7
Pages 1303-9
Authors Brandstetter H, Engh RA, Von Roedern EG, Moroder L, Huber R, Bode W, Grams F
Title Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data.
Related PDB 1a85 1a86
Related UniProtKB P22894
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9685244
Journal J Med Chem
Year 1998
Volume 41
Pages 3041-7
Authors Graf von Roedern E, Brandstetter H, Engh RA, Bode W, Grams F, Moroder L
Title Bis-substituted malonic acid hydroxamate derivatives as inhibitors of human neutrophil collagenase (MMP8).
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9781680
Journal FEBS Lett
Year 1998
Volume 436
Pages 209-12
Authors Krumme D, Wenzel H, Tschesche H
Title Hydroxamate derivatives of substrate-analogous peptides containing aminomalonic acid are potent inhibitors of matrix metalloproteinases.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10353819
Journal Biochemistry
Year 1999
Volume 38
Pages 7085-96
Authors Moy FJ, Chanda PK, Chen JM, Cosmi S, Edris W, Skotnicki JS, Wilhelm J, Powers R
Title NMR solution structure of the catalytic fragment of human fibroblast collagenase complexed with a sulfonamide derivative of a hydroxamic acid compound.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10353844
Journal Biochemistry
Year 1999
Volume 38
Pages 7332-8
Authors Farr M, Pieper M, Calvete J, Tschesche H
Title The N-terminus of collagenase MMP-8 determines superactivity and inhibition: a relation of structure and function analyzed by biomolecular interaction analysis.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-ray crystallography (1.7 Angstroms)
Medline ID
PubMed ID 10354399
Journal J Med Chem
Year 1999
Volume 42
Pages 1908-20
Authors Matter H, Schwab W, Barbier D, Billen G, Haase B, Neises B, Schudok M, Thorwart W, Schreuder H, Brachvogel V, Lonze P, Weithmann KU
Title Quantitative structure-activity relationship of human neutrophil collagenase (MMP-8) inhibitors using comparative molecular field analysis and X-ray structure analysis.
Related PDB 1bzs
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10749856
Journal J Biol Chem
Year 2000
Volume 275
Pages 18657-63
Authors Marini S, Fasciglione GF, de Sanctis G, D'Alessio S, Politi V, Coletta M
Title Cleavage of bovine collagen I by neutrophil collagenase MMP-8. Effect of pH on the catalytic properties as compared to synthetic substrates.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10930399
Journal J Biol Chem
Year 2000
Volume 275
Pages 33008-13
Authors Hiller O, Lichte A, Oberpichler A, Kocourek A, Tschesche H
Title Matrix metalloproteinases collagenase-2, macrophage elastase, collagenase-3, and membrane type 1-matrix metalloproteinase impair clotting by degradation of fibrinogen and factor XII.
Related PDB
Related UniProtKB
[17]
Resource
Comments crystal structures using synchrotron radiation
Medline ID
PubMed ID 10978185
Journal J Med Chem
Year 2000
Volume 43
Pages 3377-85
Authors Gavuzzo E, Pochetti G, Mazza F, Gallina C, Gorini B, D'Alessio S, Pieper M, Tschesche H, Tucker PA
Title Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design.
Related PDB 1i73 1i76
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11023917
Journal Biophys J
Year 2000
Volume 79
Pages 2138-49
Authors Fasciglione GF, Marini S, D'Alessio S, Politi V, Coletta M
Title pH- and temperature-dependence of functional modulation in metalloproteinases. A comparison between neutrophil collagenase and gelatinases A and B.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-ray crystallography (1.8 Angstroms)
Medline ID
PubMed ID 11278347
Journal J Biol Chem
Year 2001
Volume 276
Pages 17405-12
Authors Brandstetter H, Grams F, Glitz D, Lang A, Huber R, Bode W, Krell HW, Engh RA
Title The 1.8-A crystal structure of a matrix metalloproteinase 8-barbiturate inhibitor complex reveals a previously unobserved mechanism for collagenase substrate recognition.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11575929
Journal J Mol Biol
Year 2001
Volume 312
Pages 743-51
Authors Nar H, Werle K, Bauer MM, Dollinger H, Jung B
Title Crystal structure of human macrophage elastase (MMP-12) in complex with a hydroxamic acid inhibitor.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11563922
Journal J Med Chem
Year 2001
Volume 44
Pages 3231-43
Authors Schroder J, Henke A, Wenzel H, Brandstetter H, Stammler HG, Stammler A, Pfeiffer WD, Tschesche H
Title Structure-based design and synthesis of potent matrix metalloproteinase inhibitors derived from a 6H-1,3,4-thiadiazine scaffold.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11953425
Journal J Biol Chem
Year 2002
Volume 277
Pages 23123-30
Authors Gioia M, Fasciglione GF, Marini S, D'Alessio S, De Sanctis G, Diekmann O, Pieper M, Politi V, Tschesche H, Coletta M
Title Modulation of the catalytic activity of neutrophil collagenase MMP-8 on bovine collagen I. Role of the activation cleavage and of the hemopexin-like domain.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12011042
Journal J Biol Chem
Year 2002
Volume 277
Pages 27378-84
Authors Tsukada H, Pourmotabbed T
Title Unexpected crucial role of residue 272 in substrate specificity of fibroblast collagenase.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the peptidase family-M10A. Moreover, this enzyme belongs to Matrix metalloproteinases (MMP-8).
According to the literature [4], the catalysis proceeds through the following steps:
(1) the general base (Glu198) catalyzes the nucleophilic attack of a zinc-ligated water molecule on the carbonyl group of the scissile peptide bond.
(2) the carboxy anion of the tetrahedral transition state must be stabilized.
(3) the same residue (Glu198) mediates the transfer of its proton to the leaving amino group, giving rise to the product.
However, another paper [15] suggested the role of Glu198 is still a matter of debate, based on the experimental results of homologous enzyme, matrilysin (MMP-7; see S00395 in EzCatDB).
The pKa of Glu198 must be quite high, due to its hydrophobic environment, which is similar to that of matrilysin (S00395 in EzCatDB), suggesting that the sidechain of this residue must be protonated. Thus, Glu198 is unlikely to act as a general base, in the first place.

Created Updated
2002-08-29 2009-02-26