5UE5 | pdb_00005ue5

proMMP-7 with heparin octasaccharide bound to the catalytic domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 16 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

Validation slider image for 5UE5

This is version 2.1 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.str.2017.05.019
  • Primary Citation Related Structures: 
    5UE2, 5UE5

  • 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.


  • Organizational Affiliation
    • Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.

Macromolecule Content 

  • Total Structure Weight: 30.13 kDa 
  • Atom Count: 2,087 
  • Modeled Residue Count: 247 
  • Deposited Residue Count: 247 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Matrilysin247Homo sapiensMutation(s): 0 
Gene Names: MMP7MPSL1PUMP1
EC: 3.4.24.23
UniProt & NIH Common Fund Data Resources
Find proteins for P09237 (Homo sapiens)
Explore P09237 
Go to UniProtKB:  P09237
PHAROS:  P09237
GTEx:  ENSG00000137673 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09237
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
8N/A
Glycosylation Resources
GlyTouCan: G40559JB
GlyCosmos: G40559JB

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 16 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM057289

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Structure summary