7V5S | pdb_00007v5s

Crystal structure of human bleomycin hydrolase C73A mutant

• PDB DOI: https://doi.org/10.2210/pdb7V5S/pdb

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


• Deposited: 2021-08-18 Released: 2022-06-29 
• Deposition Author(s): Chang, C.Y., Zheng, Y.Z., Huang, S.J., Wang, Y.L., Toh, S.I., Lin, E.C.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The Structure-Function Relationship of Human Bleomycin Hydrolase: Mutation of a Cysteine Protease into a Serine Protease.

Zheng, Y.Z., Cui, J., Wang, Y.L., Huang, S.J., Lin, E.C., Huang, S.C., Rudolf, J.D., Yan, X., Chang, C.Y.

(2022) Chembiochem 23: e202200186-e202200186

• PubMed: 35467071 
• DOI: https://doi.org/10.1002/cbic.202200186
• Primary Citation Related Structures: 
  7V5L, 7V5S, 7V5T, 7XF9


• PubMed Abstract: 
  

  Human bleomycin hydrolase (hBH) catalyzes deamidation of the anticancer drug bleomycins (BLM). This enzyme is involved in BLM detoxification and drug resistance. Herein, we report the putative BLM-binding site and catalytic mechanism of hBH. The crystal structures and biochemical studies suggest that hBH cleaves its C-terminal residue without significant preference for the type of amino acid, and therefore can accordingly accommodate the β-aminoalanine amide moiety of BLM for deamidation. Interestingly, hBH is capable of switching from a cysteine protease to a serine protease that is unable to cleave the secondary amide of hBH C-terminus but reacts with the primary amide of BLMs.

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Organizational Affiliation: 
• Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan.
State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan.
Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7011, USA.
Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan.
Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.11 kDa 
• Atom Count: 3,726 
• Modeled Residue Count: 454 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bleomycin hydrolase	A	475	Homo sapiens	Mutation(s): 1  Gene Names: BLMH EC: 3.4.22.40
UniProt & NIH Common Fund Data Resources
Find proteins for Q13867 (Homo sapiens) Explore Q13867  Go to UniProtKB:  Q13867
PHAROS:  Q13867 GTEx:  ENSG00000108578

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4 (Subject of Investigation/LOI)	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE (Subject of Investigation/LOI)	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 318.269	α = 90
b = 318.269	β = 90
c = 318.269	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Chang, C.Y., Zheng, Y.Z., Huang, S.J., Wang, Y.L., Toh, S.I., Lin, E.C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	110-2113-M-A49 -026 -MY3

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description