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- PDB-9whu: Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, ... -

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Basic information

Entry
Database: PDB / ID: 9whu
TitleStructure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, trimer
Components
  • Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA polymerase theta (Helicase domain only)
KeywordsDNA BINDING PROTEIN/DNA / ATPase / Helicase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


helicase activity / nucleic acid binding / hydrolase activity / ATP binding
Similarity search - Function
Anti-bacteriophage protein A/HamA, C-terminal domain / HamA / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily ...Anti-bacteriophage protein A/HamA, C-terminal domain / HamA / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA polymerase theta (Helicase domain only) / Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHuang, P.P. / Liu, J.X. / Shen, L.B. / Chen, M.R. / Xiao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2026
Title: The antiphage mechanism of a widespread trypsin-MBL defense module.
Authors: Pingping Huang / Jingxian Liu / Lijie Guo / Dongyang Xu / Lingbo Shen / Purui Yan / Chen Tong / Wenying Fei / Mengjun Cheng / Zhaoxing Li / Meiling Lu / Lei Zhang / Nannan Wu / Lian-Wen Qi / ...Authors: Pingping Huang / Jingxian Liu / Lijie Guo / Dongyang Xu / Lingbo Shen / Purui Yan / Chen Tong / Wenying Fei / Mengjun Cheng / Zhaoxing Li / Meiling Lu / Lei Zhang / Nannan Wu / Lian-Wen Qi / Yibei Xiao / Meirong Chen /
Abstract: Protease-mediated activation of immune effectors is an evolutionarily conserved mechanism. This study identifies a widespread trypsin-MBL (metallo-β-lactamase) module as a core effector in diverse ...Protease-mediated activation of immune effectors is an evolutionarily conserved mechanism. This study identifies a widespread trypsin-MBL (metallo-β-lactamase) module as a core effector in diverse antiviral bacterial immune systems, such as Hachiman, AVAST and Argonaute. Focusing on the Hachiman-associated trypsin-MBL system, we show that trypsin•HamAB protease activity is inhibited by ATP, while MBL is an autoinhibited DNase with two insertion loops obstructing its catalytic site. Upon infection, trypsin•HamAB senses foreign DNA and hydrolyzes ATP, activating trypsin-like activity, which specifically cleaves MBL at the insertion loops to release repression. The activated MBL depletes DNA and arrests host cell growth. Cryo-electron microscopy structures of trypsin•HamAB-DNA reveal that DNA binding and ATP hydrolysis trigger HamAB oligomerization and trypsin-like domain release, enabling its activation. Our work elucidates a conserved immune mechanism wherein proteolytic activation of a nuclease enables robust immunity against phage while multilayered controls prevent self-toxicity, expanding the repertoire of immune processes governed by regulatory proteolysis.
History
DepositionAug 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
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Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
B: DNA polymerase theta (Helicase domain only)
D: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
E: DNA polymerase theta (Helicase domain only)
F: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
G: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
H: DNA polymerase theta (Helicase domain only)
I: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)483,0219
Polymers483,0219
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Anti-bacteriophage protein A/HamA C-terminal domain-containing protein / HamA


Mass: 59614.848 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: SAMEA4873653_00088 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A486PDC8
#2: Protein DNA polymerase theta (Helicase domain only) / HamB


Mass: 99035.922 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: B6I68_29715, SAMEA4873653_00087 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A486PCQ5
#3: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2147.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
#4: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2460.697 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Klebsiella pneumoniae HamAB trimer bound with DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50060 / Symmetry type: POINT
RefinementCross valid method: NONE

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