Function and Biology

Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B).

Source organism: Homo sapiens
Biochemical function: zinc ion binding
Biological process: proteolysis
Cellular component: extracellular matrix

EC 3.4.24.35: Gelatinase B

Reaction catalysed:
Cleavage of gelatin types I and V and collagen types IV and V.
Systematic name:
-
Alternative Name(s):
  • 92-kDa gelatinase
  • 92-kDa type IV collagenase
  • 95 kDa type IV collagenase/gelatinase
  • Collagenase IV
  • Collagenase type IV
  • Gelatinase MMP 9
  • MMP 9
  • Macrophage gelatinase
  • Matrix metalloproteinase 9
  • Type IV collagen metalloproteinase
  • Type V collagenase

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00040
Domain description: Fibronectin type II domain
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 3 copies of Pfam domain PF00040 (Fibronectin type II domain) in 67 kDa matrix metalloproteinase-9. Showing 3 copies in chain A.

PF00413
Domain description: Matrixin
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 1 copy of Pfam domain PF00413 (Matrixin) in 67 kDa matrix metalloproteinase-9. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR000562
Domain description: Fibronectin type II domain
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR021190
Domain description: Peptidase M10A
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR013806
Domain description: Kringle-like fold
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR036943
Domain description: Fibronectin type II domain superfamily
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR024079
Domain description: Metallopeptidase, catalytic domain superfamily
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR033739
Domain description: Peptidase M10A, catalytic domain
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR001818
Domain description: Peptidase M10, metallopeptidase
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR006026
Domain description: Peptidase, metallopeptidase
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR021158
Domain description: Peptidase M10A, cysteine switch, zinc binding site
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR002477
Domain description: Peptidoglycan binding-like
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
IPR036365
Domain description: PGBD-like superfamily
Occurring in:
  1. 67 kDa matrix metalloproteinase-9

Structure domains

CATH CATH domains
2.10.10.10
Class: Mainly Beta
Architecture: Ribbon
Topology: Seminal Fluid Protein PDC-109 (Domain B)
Homology: Fibronectin, type II, collagen-binding
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 3 copies of CATH domain 2.10.10.10 (Seminal Fluid Protein  PDC-109 (Domain B)) in 67 kDa matrix metalloproteinase-9. Showing 3 copies in chain A.
3.40.390.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Collagenase (Catalytic Domain)
Homology: Collagenase (Catalytic Domain)
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 1 copy of CATH domain 3.40.390.10 (Collagenase (Catalytic Domain)) in 67 kDa matrix metalloproteinase-9. Showing 1 copy in chain A.
1.10.101.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Muramoyl-pentapeptide Carboxypeptidase; domain 1
Homology: PGBD-like superfamily/PGBD
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 1 copy of CATH domain 1.10.101.10 (Muramoyl-pentapeptide Carboxypeptidase; domain 1) in 67 kDa matrix metalloproteinase-9. Showing 1 copy in chain A.
SCOP SCOP annotations
57459
Class: Small proteins
Fold: Kringle-like
Superfamily: Kringle-like
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 3 copies of SCOP domain 57459 (Fibronectin type II module) in 67 kDa matrix metalloproteinase-9. Showing 3 copies in chain A.
55528
Class: Alpha and beta proteins (a+b)
Fold: Zincin-like
Superfamily: Metalloproteases ("zincins"), catalytic domain
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 1 copy of SCOP domain 55528 (Matrix metalloproteases, catalytic domain) in 67 kDa matrix metalloproteinase-9. Showing 1 copy in chain A.
63427
Class: All alpha proteins
Fold: PGBD-like
Superfamily: PGBD-like
Occurring in:
  1. 67 kDa matrix metalloproteinase-9
The deposited structure of PDB entry 1l6j contains 1 copy of SCOP domain 63427 (MMP N-terminal domain) in 67 kDa matrix metalloproteinase-9. Showing 1 copy in chain A.