4ZJB

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) in complex with holo-ACP from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of FabZ-ACP complex reveals a dynamic seesaw-like catalytic mechanism of dehydratase in fatty acid biosynthesis.

Zhang, L.Xiao, J.Xu, J.Fu, T.Cao, Z.Zhu, L.Chen, H.Z.Shen, X.Jiang, H.Zhang, L.

(2016) Cell Res 26: 1330-1344

  • DOI: 10.1038/cr.2016.136
  • Primary Citation of Related Structures:  
    4ZJB

  • PubMed Abstract: 
  • Fatty acid biosynthesis (FAS) is a vital process in cells. Fatty acids are essential for cell assembly and cellular metabolism. Abnormal FAS directly correlates with cell growth delay and human diseases, such as metabolic syndromes and various cancer ...

    Fatty acid biosynthesis (FAS) is a vital process in cells. Fatty acids are essential for cell assembly and cellular metabolism. Abnormal FAS directly correlates with cell growth delay and human diseases, such as metabolic syndromes and various cancers. The FAS system utilizes an acyl carrier protein (ACP) as a transporter to stabilize and shuttle the growing fatty acid chain throughout enzymatic modules for stepwise catalysis. Studying the interactions between enzymatic modules and ACP is, therefore, critical for understanding the biological function of the FAS system. However, the information remains unclear due to the high flexibility of ACP and its weak interaction with enzymatic modules. We present here a 2.55 Å crystal structure of type II FAS dehydratase FabZ in complex with holo-ACP, which exhibits a highly symmetrical FabZ hexamer-ACP 3 stoichiometry with each ACP binding to a FabZ dimer subunit. Further structural analysis, together with biophysical and computational results, reveals a novel dynamic seesaw-like ACP binding and catalysis mechanism for the dehydratase module in the FAS system, which is regulated by a critical gatekeeper residue (Tyr100 in FabZ) that manipulates the movements of the β-sheet layer. These findings improve the general understanding of the dehydration process in the FAS system and will potentially facilitate drug and therapeutic design for diseases associated with abnormalities in FAS.


    Organizational Affiliation

    Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZAB171Helicobacter pyloriMutation(s): 0 
Gene Names: 
EC: 4.2.1.59
Find proteins for Q5G940 (Helicobacter pylori)
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Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinG86Helicobacter pyloriMutation(s): 0 
Gene Names: 
acpPEG63_02640HPY173_03440HPY1786_00110HPY1846_06495HPY207_02635HPY228_03880HPY499_02145JM68_05695acpP_2AA971_03770AC783_02170AC784_02620AC786_00270ACM24_03385ACM26_04180ACM29_06640ACM31_06735ACM32_06930ACM37_01955AEY53_01410AEY54_07605AEY55_04590AK968_06385AM496_03540AM497_00990AOD77_0205430AP069_0203010APV63_03895AV920_0203940AV921_0203680B0X29_03800B0X34_06465B0X34_08305B0X35_04970B0X36_01550B0X43_06585B0X45_00570B0X60_00365B0X65_03745B0X68_05455BB384_06970BB390_02880BB395_06520BB397_06510BB407_06715BB411_01045BB413_00115BB414_01745BB425_06615BB438_02555BB445_05830BB447_03590BB453_06290BB458_02285BB461_04255BB464_01665BB465_07345BGL56_05060BGL58_01775BGL66_01950BGL69_04330BGL75_08125BHU51_05610BV499_06310BZK21_01490BZK27_00480C2R44_07500C2R53_03535C2R57_06525C2R62_01950C2R66_01755C2R70_06095C2R82_01455C2R85_07050C2R93_06190C2R96_08170C2S01_06755C2S04_07420C2S07_01945C2S19_07900C2S29_06635C2S30_06165C2S39_07050C2S42_07730C2S44_03705C2S49_04670CGC32_03355CV726_04705CV727_03490CV728_03285CV729_03805CV730_03675D2C75_01225D2C78_06425D2C82_03205D2C86_05180D8X56_02965DD744_02950DD748_03425DD749_02975DD750_02355DD759_02770DD773_02150DD777_02295DD779_02830DD780_02775DDP32_03230DDP35_03120DDP37_03425DDP39_02640DDP42_02985DDP43_02890DDP44_02790DDP47_01920DDP49_02455DDP51_02995DDP52_03495DDP57_02830DZC36_03360EC503_03190EC505_03755EC507_02220EC511_02300EC513_03025EC517_03570EC518_00005EC525_03720EC532_06155EC533_02570EC537_03220EC546_03665EC547_02800EC550_02360EC552_02515EC554_05615EC556_02625EC558_03510EC565_04600EC572_05195EC584_05040EC585_03955EC589_03210EC590_01945EC592_04700ECB90_05815ECC07_01920ECC12_02075ECC16_05650ECC17_03030ECC22_04550ECC24_01300ECC32_05485ECC33_03205ECC34_03320ECC35_03300ECC37_03185ECC38_04160ECC40_02350ECC41_02110ECC43_03930ECC44_01495ECC45_04300ECC49_04200ECE45_03160ECE49_00260EDA74_03725EDB75_01310EDC13_02400EE66_03620EGM90_01110EGV98_07325EGW00_04210EGW01_07925EPC79_07230EPC80_01035F7197_04985F7213_06745F7220_05045F7226_05330F7229_06460GOM66_03930HPF17_0447HPF209_0807HPF210_0847HPF72_0568HPK21_01210HPMKM5_0823HPPMSS1_c00678NCTC13207_00771OA23_03965

Find proteins for Q5EDC8 (Helicobacter pylori)
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS

Download CCD File 
G
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.705α = 90
b = 127.705β = 90
c = 127.705γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data processing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references