2JIH

Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine- Rich Domain (complex-form)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structures of human ADAMTS-1 reveal a conserved catalytic domain and a disintegrin-like domain with a fold homologous to cysteine-rich domains.

Gerhardt, S., Hassall, G., Hawtin, P., McCall, E., Flavell, L., Minshull, C., Hargreaves, D., Ting, A., Pauptit, R.A., Parker, A.E., Abbott, W.M.

(2007) J Mol Biol 373: 891-902

  • DOI: 10.1016/j.jmb.2007.07.047
  • Primary Citation of Related Structures:  
    2JIH, 2V4B

  • PubMed Abstract: 

    • The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type I motifs) family of proteases plays a role in pathological conditions including arthritis, cancer, thrombotic thrombocytopenic purpura and the Ehlers-Danlos type VIIC and Weill-Marchesani genetic syndromes ...

    The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type I motifs) family of proteases plays a role in pathological conditions including arthritis, cancer, thrombotic thrombocytopenic purpura and the Ehlers-Danlos type VIIC and Weill-Marchesani genetic syndromes. Here, we report the first crystal structures for a member of the ADAMTS family, ADAMTS-1. Originally cloned as an inflammation-associated gene, ADAMTS-1 has been shown to be involved in tissue remodelling, wound healing and angiogenesis. The crystal structures contain catalytic and disintegrin-like domains, both in the inhibitor-free form and in complex with the inhibitor marimastat. The overall fold of the catalytic domain is similar to related zinc metalloproteinases such as matrix metalloproteinases and ADAMs (a disintegrin and metalloproteinases). The active site contains the expected organisation of residues to coordinate zinc but has a much larger S1' selectivity pocket than ADAM33. The structure also unexpectedly reveals a double calcium-binding site. Also surprisingly, the previously named disintegrin-like domain showed no structural homology to the disintegrin domains of other metalloproteinases such as ADAM10 but is instead very similar in structure to the cysteine-rich domains of other metalloproteinases. Thus, this study suggests that the D (for disintegrin-like) in the nomenclature of ADAMTS enzymes is likely to be a misnomer. The ADAMTS-1 cysteine-rich domain stacks against the active site, suggesting a possible regulatory role.

    Organizational Affiliation: 

    Global Structural Chemistry, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADAMTS-1A, B300Homo sapiensMutation(s): 0 
Gene Names: ADAMTS1, KIAA1346, METH1
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI8 (Homo sapiens)
Explore Q9UHI8 
Go to UniProtKB:  Q9UHI8
PHAROS:  Q9UHI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHI8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
097
Query on 097
Download Ideal Coordinates CCD File 
C [auth A],
U [auth B]		(2S,3R)-N~4~-[(1S)-2,2-dimethyl-1-(methylcarbamoyl)propyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide
C15 H29 N3 O5
OCSMOTCMPXTDND-OUAUKWLOSA-N		 Ligand Interaction
CD
Query on CD
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth A],
I [auth A],
W [auth B],
E [auth A],
F [auth A],
H [auth A],
I [auth A],
W [auth B],
Y [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
V [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
NI
Query on NI
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AA [auth B],
CA [auth B],
EA [auth B],
G [auth A],
J [auth A],
AA [auth B],
CA [auth B],
EA [auth B],
G [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
S [auth A],
X [auth B],
Z [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
BA [auth B],
DA [auth B],
HA [auth B],
IA [auth B],
K [auth A],
BA [auth B],
DA [auth B],
HA [auth B],
IA [auth B],
K [auth A],
T [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
FA [auth B],
GA [auth B],
P [auth A],
Q [auth A],
R [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.579α = 90
b = 64.396β = 90.91
c = 113.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2019-04-24
    Changes: Data collection, Source and taxonomy