4JGC

Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC)

> Summary

Summary for 4JGC

Related4FNC
DescriptorG/T mismatch-specific thymine DNA glycosylase, oligonucleotide, oligonucleotide containing 5-carboxylcytosine, ... (5 entities in total)
Functional Keywords5-carboxylcytosine; thymine dna glycosylase; dna modification; dna 5mc oxidation; epigenetic regulation, dna demethylation, 5-carboxylcytosine, hydrolase-dna complex, hydrolase/dna
Biological sourceHomo sapiens (human)
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Cellular locationNucleus Q13569
Total number of polymer chains3
Total molecular weight40302.75
Authors
Hashimoto, H.,Zhang, X.,Cheng, X. (deposition date: 2013-02-28, release date: 2013-05-29, Last modification date: 2013-07-03)
Primary citation
Hashimoto, H.,Zhang, X.,Cheng, X.
Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH.
Dna Repair, 12:535-540, 2013
PubMed: 23680598 (PDB entries with the same primary citation)
DOI: 10.1016/j.dnarep.2013.04.003
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.582 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2921202.5%3.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4jgc
no rotation
Molmil generated image of 4jgc
rotated about x axis by 90°
Molmil generated image of 4jgc
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AG/T mismatch-specific thymine DNA glycosylasepolymer20423027.61
UniProt (Q13569)
Pfam (PF03167)
Homo sapiens (human)@PDBjThymine-DNA glycosylase
Coligonucleotidepolymer288646.61
Doligonucleotide containing 5-carboxylcytosinepolymer288473.41
4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acidnon-polymer155.11
waterwater18.022

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight40147.6
Non-Polymers*Number of molecules1
Total molecular weight155.1
All*Total molecular weight40302.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.582 Å)

Cell axes91.48653.55581.902
Cell angles90.0095.1090.00
SpacegroupC 1 2 1
Resolution limits45.56 - 2.58
the highest resolution shell value2.842 - 2.582
R-factor0.2324
R-work0.22980
the highest resolution shell value0.383
R-free0.28330
the highest resolution shell value0.399
RMSD bond length0.019
RMSD bond angle1.196

Data Collection Statistics

Resolution limits45.56 - 2.58
the highest resolution shell value -
Number of reflections11604
Rmerge_l_obs0.077
the highest resolution shell value0.365
Completeness92.9
Redundancy4
the highest resolution shell value2.8
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION4.6289

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005886cellular_componentplasma membrane
A0016605cellular_componentPML body
A0005524molecular_functionATP binding
A0031404molecular_functionchloride ion binding
A0003684molecular_functiondamaged DNA binding
A0003677molecular_functionDNA binding
A0019104molecular_functionDNA N-glycosylase activity
A0003690molecular_functiondouble-stranded DNA binding
A0043739molecular_functionG/U mismatch-specific uracil-DNA glycosylase activity
A0000287molecular_functionmagnesium ion binding
A0030983molecular_functionmismatched DNA binding
A0019904molecular_functionprotein domain specific binding
A0042803molecular_functionprotein homodimerization activity
A0005080molecular_functionprotein kinase C binding
A0043621molecular_functionprotein self-association
A0008263molecular_functionpyrimidine-specific mismatch base pair DNA N-glycosylase activity
A0001104molecular_functionRNA polymerase II transcription cofactor activity
A0031402molecular_functionsodium ion binding
A0032183molecular_functionSUMO binding
A0008134molecular_functiontranscription factor binding
A0004844molecular_functionuracil DNA N-glycosylase activity
A0006284biological_processbase-excision repair
A0006285biological_processbase-excision repair, AP site formation
A0016569biological_processcovalent chromatin modification
A0045008biological_processdepyrimidination
A0080111biological_processDNA demethylation
A0009790biological_processembryo development
A0006298biological_processmismatch repair
A0035562biological_processnegative regulation of chromatin binding
A0032091biological_processnegative regulation of protein binding
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0035511biological_processoxidative DNA demethylation
A1902544biological_processregulation of DNA N-glycosylase activity
A0040029biological_processregulation of gene expression, epigenetic
A0006351biological_processtranscription, DNA-templated
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC110BINDING SITE FOR RESIDUE 1RT D 417
ChainResidue
AGLY138
AILE139
AALA140
APRO141
AGLY142
ATYR152
AASN191
AASN230
ASER271
DORP17

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
1RT_4jgc_D_417164-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID binding site
ChainResidueligand
AILE137-GLY1421RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
AALA1451RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
ATYR1521RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
AASN1911RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
AASN230-GLY2311RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
ASER271-SER2731RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID
DORP17-DG181RT: 4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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