[English] 日本語
Yorodumi
- PDB-3uth: Crystal structure of Aspergillus fumigatus UDP galactopyranose mu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uth
TitleCrystal structure of Aspergillus fumigatus UDP galactopyranose mutase complexed with substrate UDP-Galp in reduced state
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / Nucleotide binding / Mutase / Flavin adenine dinucleotide binding
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding
Similarity search - Function
NAD(P)-binding Rossmann-like domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDhatwalia, R. / Singh, H. / Tanner, J.J.
CitationJournal: J Biol Chem / Year: 2012
Title: Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus.
Authors: Richa Dhatwalia / Harkewal Singh / Michelle Oppenheimer / Dale B Karr / Jay C Nix / Pablo Sobrado / John J Tanner /
Abstract: UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. ...UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM has several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 Å to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-galactopyranose mutase
B: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,95022
Polymers228,5144
Non-polymers5,43618
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-236 kcal/mol
Surface area73540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.125, 219.125, 322.428
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein
UDP-galactopyranose mutase


Mass: 57128.484 Da / Num. of mol.: 4 / Mutation: K344A, K345A, A429T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: glf, glfA / Plasmid: pVP56K / Production host: Escherichia coli (E. coli) / References: UniProt: Q4W1X2, UDP-galactopyranose mutase
#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT A429T IS AN UNINTENDED MUTATION ON THE SURFACE OF THE PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.89 Å3/Da / Density % sol: 74.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.5M ammonium sulfate, 0.1M sodium acetate, 5mM L-cysteine, 0.5mM THP , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2011
Details: Cryogenically-cooled single crystal Si(220) side bounce monochromator. Optional Si(311) to achive 13.474 keV.
RadiationMonochromator: Cryo-Cooled double crystal. / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.25→48.807 Å / Num. all: 207614 / Num. obs: 207614 / % possible obs: 97.3 % / Redundancy: 8 % / Rsym value: 0.097 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.3770.5991.3211674301250.59997.6
2.37-2.527.50.421.9215731286150.4297.9
2.52-2.6980.3052.6215181269240.30598.1
2.69-2.98.40.213.7210094251020.2197.9
2.9-3.188.60.1425.4197802230340.14297.3
3.18-3.568.60.0987.5178416207710.09896.7
3.56-4.118.40.0729.7153919183220.07296.3
4.11-5.038.10.05911.5126397155890.05996.3
5.03-7.128.40.04913.9103242122360.04996.6
7.12-48.8078.40.03215.35769568960.03295.2

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTE

3ute


Resolution: 2.25→48.807 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8717 / SU ML: 0.32 / σ(F): 0 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 10394 5.01 %based on test set used for refinement of AfUGM-sulfate complex of the same enzyme
Rwork0.1855 ---
obs0.1868 207473 96.97 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.824 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 125.46 Å2 / Biso mean: 35.5875 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--5.535 Å2-0 Å20 Å2
2---5.535 Å2-0 Å2
3---11.0701 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15562 0 344 659 16565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716310
X-RAY DIFFRACTIONf_angle_d1.07722301
X-RAY DIFFRACTIONf_chiral_restr0.072453
X-RAY DIFFRACTIONf_plane_restr0.0052874
X-RAY DIFFRACTIONf_dihedral_angle_d17.8546031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.33040.294510310.2489195852061697
2.3304-2.42370.27310160.234195882060498
2.4237-2.5340.255610450.2146196632070898
2.534-2.66760.257710630.211196912075498
2.6676-2.83470.234410100.1955197422075298
2.8347-3.05360.233810320.1994196842071697
3.0536-3.36080.232710430.2059196332067697
3.3608-3.84690.209310450.1891195802062596
3.8469-4.84610.159610320.1418197142074696
4.8461-48.81830.17410770.1648201992127695
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5346-0.105-0.03620.01760.00530.2006-0.00610.14490.00890.0512-0.0226-0.060.01-0.0307-0.00190.09270.02180.04240.2305-0.01520.217472.091478.2478161.13
20.1724-0.24440.01480.3325-0.02060.2226-0.07350.0093-0.00590.07850.03480.0596-0.0070.0067-0.00150.17610.04250.00760.1338-0.02950.169924.7329104.0044213.4757
30.61930.0447-0.00210.1320.03250.1488-0.00470.2217-0.11340.04650.03310.00170.04380.0148-0.00130.11750.0224-0.02850.2938-0.08870.162425.853868.6989151.1966
40.225-0.33280.05290.534-0.00470.164-0.0842-0.0065-0.09790.16650.10150.1050.01280.00740.00160.2050.05630.03220.1560.06120.1742.619360.2619223.8815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 507
2X-RAY DIFFRACTION2chain BB3 - 507
3X-RAY DIFFRACTION3chain CC3 - 506
4X-RAY DIFFRACTION4chain DD3 - 507

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more