Zengqiang Gao

Chinese Academy of Sciences | CAS

Recent technological breakthroughs in machine-learning-based AlphaFold2 (AF2) are pushing the prediction accuracy of protein structures to an unprecedented level that is on par with experimental structural quality. Despite its outstanding structural modeling capability, further experimental validations and performance assessments of AF2 predictions...

PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids—the main component of cell membranes—and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa. As a cognate immunity protein, PA3488 can inhibit the activity of PldA to avoid self-toxicity. However, the precise inhib...

Electron tomography, a powerful imaging tool for studying 3D structures of macromolecular assemblies, always suffers from imperfect reconstruction with limited resolution due to the intrinsic low signal-to-noise ratio (SNR) and inaccessibility to certain tilt angles induced by radiation damage or mechanical limitation. In order to compensate for su...

The genome of the thermophilic bacteriophage GVE2 encodes a putative tailspike protein (GVE2 TSP). Here we report the crystal structure of the truncated GVE2 TSP at 2.0-Å resolution lacking 204 amino acid residues at its N-terminus (ΔnGVE2 TSP), possessing a "vase" outline similar to other TSP's structures. However, ΔnGVE2 TSP displays structural c...

The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic an...

HigB-HigA is a bacterial toxin–antitoxin (TA) system in which the antitoxin HigA can mask the endoribonuclease activity of toxin HigB and repress the transcription of the TA operon by binding to its own promoter region. The opportunistic pathogen Pseudomonas aeruginosa HigBA (PaHigBA) is closely associated with the pathogenicity by reducing the pro...

Background The search of heavy atoms is crucial to the de novo determination of protein structures. Typically, the difference Patterson map is calculated as a first step to solve substructure. However, the pseudo-peaks and noises inherent in such maps arising from the high symmetry and large size of protein structures accompanied with the data coll...

Abstract The multicopper oxidase CueO is involved in copper homeostasis and copper (Cu) tolerance in Escherichia coli. The laccase activity of CueO G304K mutant is higher than wild-type CueO. To explain this increase in activity, we solved the crystal structure of G304K mutant at 1.49 Å. Compared with wild-type CueO, the G304K mutant showed dramati...

Recent advances in serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) have facilitated accurate structure determination for biological macromolecules. However, given the many fluctuations inherent in SFX, the acquisition of SFX data of sufficiently high quality still remains challenging. Aimed at enhancing the accurac...

HD-domain is a conserved domain, with the signature of histidine and aspartic (HD) residues doublets. HD-domain proteins may possess nucleotidase and phosphodiesterase activities, and they play important roles in signaling and nucleotide metabolism. In yeast, HD-domain proteins with nucleotidase activity remained unexplored. Here, we biochemically...

Toxin-antitoxin (TA) loci in bacteria are small genetic modules that regulate various cellular activities, including cell growth and death. The two-gene module encoding a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain has been predicted to represent a novel type II TA sys...

Wss1 is a DNA-protein crosslinks (DPCs) repair protein, which is responsible for degradation of the protein components in DPCs. In this investigation, crystal structure of the protease domain from saccharomyces cerevisiae Wss1 (ScWss1) was solved and was compared with the known crystal structure of Schizosaccharomyces prombe Wss1 (SpWss1). It is fo...

Toxin–antitoxin (TA) systems are widespread in both bacteria and archaea, where they enable cells to adapt to environmental cues. TA systems play crucial roles in various cellular processes, such as programmed cell death, cell growth, persistence and virulence. Here, two distinct forms of the type II toxin–antitoxin complex HicAB were identified an...

The selective in situ reactions of 1,2-di(1H-benzimidazol-2-yl)ethane-1,2-diol (TDB) in the presence of 3d transition-metal ions under hydrothermal conditions were investigated. The research demonstrated that divalent Fe, Co, and Ni salts are apt to cause the intramolecular dehydration of TDB, then form pentanuclear [M5(H2L)6]⁴⁺ clusters, and Cu ca...

RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet)-dependent methyltransferases (MTases) that are responsible for the 2′-O-methylation and N⁴-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m⁴Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently f...

Modification of C1402 in bacterial 16S rRNA by RsmI and RsmH for the 2′-O-methylation and N4-methylation, respectively. (TIF)

Crystal packing of the three RsmI molecules (the subunits I, II and III in magenta, cyan and green, respectively) in one asymmetric unit. Three RsmI molecules (the subunits I’, II’ and III’) in another asymmetric unit are shown in gray. The subunits I and II (or I’ and II’) can form a compact homodimer. The subunit III forms another dimer with its...

Comparison of the surface charge distribution of RsmI (+7.8 KT; -7.8 KT), CbiF (PDB code 1CBF, +7.2KT; -7.2KT) and CbiL (PDB code 2E0N, +7.3KT; -7.3KT), by their local electrostatic potential (positive charge in blue and negative charge in red). (TIF)

The direct interactions (within 3.9 Å) between the two subunits of RsmI dimer analyzed by PDBe-PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html). (DOCX)

Structural superimposition of RsmI (cyan) with RsmH (magenta, PDB code 3TKA) in ribbon. (TIF)

Surface presentations of wild-type RsmI (A) and the A124L mutant model (B). The adenosine ring of AdoMet shows obvious steric hindrance with L124 in the mutant model, causing its unfavorable binding to AdoMet. (TIF)

Purified RsmI (Gly12-Pro258) (A) eluted from gel filtration chromatogram (Superdex™ 200 10/300 GL) at 15.0 ml, and the elution volume of protein standards (Thermo Scientific, USA) (B) from this column. (TIF)

The toxin-antitoxin system is ubiquitously existed in bacteria and archaea, performing a wide variety of functions modulating cell fitness in response to environmental cues. In this report, we solved the crystal structure of the toxin-antitoxin HigBA complex from E. coli K-12 to 2.7 angstrom resolution. The crystal structure of the HigBA complex di...

In cells, dUMP is the intermediate precursor of dTTP in its synthesis during deoxynucleotide metabolism. In Gram-positive bacteria and eukaryotes, zinc-dependent deoxycytidylate deaminases (dCDs) catalyze the conversion of dCMP to dUMP. The activity of dCD is allosterically activated by dCTP and inhibited by dTTP. Here, the crystal structure of Str...

Toxin–antitoxin (TA) loci are widespread in bacteria plasmids and chromosomes, and target various cellular functions to regulate cell growth and death. A type II TA system RnlA-RnlB from Escherichia coli is associated with phage-resistance. After the infection of bacteriophage T4 with Dmd defection, RnlA is activated by the disappearance of RnlB, r...

Importance: Oncogenic herpesvirus KSHV is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma and multicentric Castelman's disease. KSHV has developed a unique mechanism to subvert host antiviral immune responses by encoding four homologues of cellular interferon regulatory factors (vIRF1∼4). However, none of their DNA-binding pro...

To evaluate magnetic properties of isostructural compounds, a series of 3D carboxylate coordination polymers [M(H2bpta)]n, (H4bpta = 2,2',4,4'-biphenyltetracarboxylic acid, M = Fe(II) (1), Ni(II) (2), Cu(II) (3) and Zn(II) (4)), have been synthesized in H2O/CH3CN or H2O solvents, respectively. Structurally, complexes 1−4 have isostructural features...

Sodium dodecyl sulfate (SDS) is a widely used anionic surfactant in industry and research settings, and is known to have a detrimental effect to the environment. The pathway of SDS degradation by bacteria is initiated by an alkylsulfatase and the oxidised product, 1-dodecanoic acid, subsequently enters into the β-oxidation pathway and is used as a...

A diverse superfamily of phospholipases consisting of the type VI lipase effectors Tle1–Tle5 secreted by the bacterial type VI secretion system (T6SS) have recently been identified as antibacterial effectors that hydrolyze membrane phospholipids. These effectors show no significant homology to known lipases, and their mechanism of membrane targetin...

The putative protein PA5089 from Pseudomonas aeruginosa has recently been identified as a Tle5 phospholipase effector from a type VI secretion system (T6SS), and its toxicity can be neutralized by the cognate immunity protein Tli5 (PA5088). Here, the expression, purification, crystallization and preliminary crystallographic analysis of PA5088 are r...

Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the isolated YafQ toxin have been determined. The structure of the heterotetrameric complex (DinJ)2-(Ya...

Huanglongbing (HLB) is a destructive citrus disease. The leading cause of HLB is Candidatus Liberibacter asiaticus. Fatty acid biosynthesis(FAS-II)is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterials agents. Enoyl-acyl carrier protein reductase (also called ENR or FabI and a product of th...

The RecQ helicase from Deinococcus radiodurans (DrRecQ) distinguishes from other helicases in that it utilizes its three 'helicase and RNaseD C-terminal' domains (HRDC1, HRDC2 and HRDC3) to regulate its activity. These HRDC domains have different influence on the biochemical functions of DrRecQ. Currently, only the structure of HRDC3 was reported....

Master regulators, which broadly affect expression of diverse genes, play critical roles in bacterial growth and environmental adaptation. However, the underlying mechanism by which such regulators interact with their cognate DNA remains to be elucidated. In this study, we solved the crystal structure of a broad regulator Ms6564 in Mycobacterium sm...

α(1)-Microglobulin (α(1)m) is one of the phylogenetically most widespread lipocalins and is distributed in various organs and tissues, including liver, heart, eye, kidney, brain, lung, pancreas and skeletal muscle. α(1)m has been found to exert multifarious functions, including interacting with IgA, albumin and prothrombin, binding strongly to haem...

Six copper complexes of Schiff base ligands containing 3,5-substituted-4-salicylideneamino-3,5-dimethyl-1,2,4-triazole have been synthesized and well characterized. The structures of complexes 1 and 2 were determined by X-ray crystal analysis. Fluorescence and potentiometric study indicated that in the physiological pH range, one ligand was dissoci...

The X-ray crystal structure of the cAMP-liganded D138L mutant of Escherichia coli catabolite gene activator protein (CAP) was determined at a resolution of 1.66Å. This high resolution crystal structure reveals four cAMP binding sites in the homodimer. Two anti conformations of cAMPs (anti-cAMP) locate between the β-barrel and the C-helix of each su...

Nitroalkane oxidase (NAO) catalyzes neutral nitroalkanes to their corresponding aldehydes or ketones, hydrogen peroxide and nitrite. The crystal structure of NAO from Streptomyces ansochromogenes was determined; it consists of two domains, a TIM barrel domain bound to FMN and C-terminal domain with a novel folding pattern. Site-directed mutagenesis...

The structures of proteins are very essential in understanding the functions of proteins. Protein crystallography is the most wide-used and precious method for structure determination of proteins. This chapter, Protein crystallography for metalloproteins, is divided into four sections. Firstly, we introduce protein crystallography by comparing with...