Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.44 kDa 
• Atom Count: 5226 
• Modelled Residue Count: 550 
• Deposited Residue Count: 577 
• Unique protein chains: 1

4UPI

Dimeric sulfatase SpAS1 from Silicibacter pomeroyi

• DOI: 10.2210/pdb4UPI/pdb

• Classification: HYDROLASE
• Organism(s): Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-06-17 Released: 2015-07-01 
• Deposition Author(s): Jonas, S., van Loo, B., Hollfelder, F., Hyvonen, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.163 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Literature

Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily.

van Loo, B., Bayer, C.D., Fischer, G., Jonas, S., Valkov, E., Mohamed, M.F., Vorobieva, A., Dutruel, C., Hyvonen, M., Hollfelder, F.

(2019) J Am Chem Soc 141: 370-387

• PubMed: 30497259 
• DOI: 10.1021/jacs.8b10290
• Primary Citation of Related Structures:  
  4UPH, 4UPI, 4UPK, 4UPL


• PubMed Abstract: 
  

Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 10 ¹¹ - to 10 ¹⁷ -fold for their primary and 10 ⁹ - to 10 ¹² -fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. This functional characterization and crystallography reveal a novel class of ASs that is so similar in sequence to known PMHs that it had not been recognized as having diverged in function. Based on analysis of snapshots of catalytic promiscuity "in transition", we develop possible models that would allow functional evolution and determine scenarios for trade-off between multiple activities. For the new ASs, we observe largely invariant substrate specificity that would facilitate the transition from ASs to PMHs via trade-off-free molecular exaptation, that is, evolution without initial loss of primary activity and specificity toward the original substrate. This ability to bypass low activity generalists provides a molecular solution to avoid adaptive conflict.

---

Organizational Affiliation: 

Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFATASE FAMILY PROTEIN	A	576	Ruegeria pomeroyi DSS-3	Mutation(s): 1  Gene Names: SPOA0121
Find proteins for Q5LLA5 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LLA5  Go to UniProtKB:  Q5LLA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DDZ	A	L-PEPTIDE LINKING	C3 H7 N O4		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.163 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.027	α = 90
b = 86.029	β = 115.19
c = 82.874	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-17 
• Released Date: 2015-07-01 
Deposition Author(s): Jonas, S., van Loo, B., Hollfelder, F., Hyvonen, M.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other
• Version 1.2: 2018-12-19
  Changes: Data collection, Database references
• Version 2.0: 2019-04-24
  Changes: Data collection, Derived calculations, Polymer sequence
• Version 2.1: 2019-05-08
  Changes: Data collection, Database references