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- PDB-9j22: structure of human urea transport protein slc14A1 with urea -

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Basic information

Entry
Database: PDB / ID: 9j22
Titlestructure of human urea transport protein slc14A1 with urea
ComponentsUrea transporter 1
KeywordsTRANSPORT PROTEIN / human urea transport protein slc14A1
Function / homology
Function and homology information


urea channel activity / water transmembrane transporter activity / urea transport / Transport of bile salts and organic acids, metal ions and amine compounds / urea transmembrane transporter activity / urea transmembrane transport / establishment of localization in cell / transmembrane transport / basolateral plasma membrane / plasma membrane
Similarity search - Function
Urea transporter / Urea transporter / Ammonium/urea transporter
Similarity search - Domain/homology
PALMITIC ACID / UREA / Urea transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsHe, J. / Wang, F. / Zhong, C. / Zhang, P. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentC10120180025 China
CitationJournal: J Biol Chem / Year: 2025
Title: Structural basis of the bifunctionality of Marinobacter salinexigens ZYF650 glucosylglycerol phosphorylase in glucosylglycerol catabolism.
Authors: Di Lu / Keke Zhang / Chen Cheng / Danni Wu / Lei Yin / Quan Luo / Meiyun Shi / Honglei Ma / Xuefeng Lu /
Abstract: 2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and ...2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and degrade it once the stimulus diminishes. Heterotrophic bacteria utilize GG phosphorylase (GGP), a member of the GH13_18 family, via a two-step process consisting of phosphorolysis and hydrolysis for GG catabolism. However, the precise mechanism by which GGP degrades GG remains elusive. We determined the 3D structure of a recently identified GGP (MsGGP) of the deep-sea bacterium Marinobacter salinexigens ZYF650, in complex with glucose and glycerol, α-d-glucose-1-phosphate (αGlc1-P), and orthophosphate (inorganic phosphate) at resolutions of 2.5, 2.7, and 2.7 Å, respectively. Notably, the first αGlc1-P complex structure in the GH13_18 family, the complex of MsGGP and αGlc1-P, validates that GGP catalyzes GG decomposition through consecutive phosphorolysis and hydrolysis. In addition, the structure reveals the mechanism of high stereoselectivity on αGlc1-P. Glu231 and Asp190 were identified as the catalytic residues. Interestingly, these structures closely resemble each other, indicating minimal conformational changes upon binding end-product glucose and glycerol, or the intermediate αGlc1-P. The structures also indicate that the substrates may follow a specific trajectory and a precise order toward the active center in close proximity and in a geometrically favorable orientation for catalysis in a double displacement mechanism.
History
DepositionAug 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urea transporter 1
B: Urea transporter 1
C: Urea transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,67630
Polymers127,6983
Non-polymers3,97827
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 Urea transporter 1 / urea transport protein slc14A1 / Solute carrier family 14 member 1 / Urea transporter / erythrocyte


Mass: 42566.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC14A1, HUT11, JK, RACH1, UT1, UTE / Production host: Baculoviridae sp. (virus) / References: UniProt: Q13336
#2: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Complex of human urea transport protein slc14A1 with urea
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Baculoviridae sp. (virus)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
EM embeddingMaterial: water
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5127: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348046 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028439
ELECTRON MICROSCOPYf_angle_d0.4311442
ELECTRON MICROSCOPYf_dihedral_angle_d6.9941251
ELECTRON MICROSCOPYf_chiral_restr0.0371308
ELECTRON MICROSCOPYf_plane_restr0.0041386

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