Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.13 kDa 
• Atom Count: 2087 
• Residue Count: 247 
• Unique protein chains: 1

5UE2

proMMP-7 with heparin octasaccharide bridging between domains

• DOI: 10.2210/pdb5UE2/pdb
• BMRB: 25485

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-12-29 Released: 2017-07-19 
• Deposition Author(s): Fulcher, Y.G., Prior, S.H., Linhardt, R.J., Van Doren, S.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 120 
• Conformers Submitted: 16 
• Selection Criteria: structures with the least restraint violations 

Literature

Glycan Activation of a Sheddase: Electrostatic Recognition between Heparin and proMMP-7.

Fulcher, Y.G., Prior, S.H., Masuko, S., Li, L., Pu, D., Zhang, F., Linhardt, R.J., Van Doren, S.R.

(2017) Structure 25: 1100-1110.e5

• PubMed: 28648610 
• DOI: 10.1016/j.str.2017.05.019
• Primary Citation of Related Structures:  
  5UE5, 5UE2


• PubMed Abstract: 
  

Heparan sulfate proteoglycans activate the matrix metalloproteinase-7 zymogen (proMMP-7) and recruit it in order to shed proteins from cell surfaces. This occurs in uterine and mammary epithelia, bacterial killing, lung healing, and tumor cell signaling. Basic tracks on proMMP-7 recognize polyanionic heparin, according to nuclear magnetic resonance and mutations disruptive of maturation. Contacts and proximity measurements guided docking of a heparin octasaccharide to proMMP-7. The reducing end fits into a basic pocket in the pro-domain while the chain continues toward the catalytic domain. Another oligosaccharide traverses a basic swath remote on the catalytic domain and inserts its reducing end into a slot formed with the basic C terminus. This latter association appears to support allosteric acceleration of proteolysis. The modes of binding account for extended, heterogeneous assemblies of proMMP-7 with heparinoids during maturation and for bridging to pro-α-defensins and proteoglycans. These associations support proteolytic release of activities at epithelial cell surfaces.

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Related Citations: 

• Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors.
  Prior, S.H., Fulcher, Y.G., Koppisetti, R.K., Jurkevich, A., Van Doren, S.R.
  (2015) Structure 23: 2099

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Organizational Affiliation: 

Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrilysin	A	247	Homo sapiens	Mutation(s): 1  Gene Names: MMP7, MPSL1, PUMP1 EC: 3.4.24.23
Find proteins for P09237 (Homo sapiens) Explore P09237  Go to UniProtKB:  P09237
NIH Common Fund Data Resources
PHAROS:  P09237 GTEx:  ENSG00000137673

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	B	8		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 120 
• Conformers Submitted: 16 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 5UE2 Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-12-29 
• Released Date: 2017-07-19 
Deposition Author(s): Fulcher, Y.G., Prior, S.H., Linhardt, R.J., Van Doren, S.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM057289

Revision History 

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary