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2ZWA

Crystal structure of tRNA wybutosine synthesizing enzyme TYW4

Functional Information from GO Data
ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0006400biological_processtRNA modification
A0008033biological_processtRNA processing
A0008168molecular_functionmethyltransferase activity
A0008175molecular_functiontRNA methyltransferase activity
A0030488biological_processtRNA methylation
A0031591biological_processwybutosine biosynthetic process
A0032259biological_processmethylation
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0006400biological_processtRNA modification
B0008033biological_processtRNA processing
B0008168molecular_functionmethyltransferase activity
B0008175molecular_functiontRNA methyltransferase activity
B0030488biological_processtRNA methylation
B0031591biological_processwybutosine biosynthetic process
B0032259biological_processmethylation
Functional Information from PDB Data
site_idAC1
Number of Residues24
DetailsBINDING SITE FOR RESIDUE SAH A 801
ChainResidue
AILE27
AGLY117
AASP146
ATYR147
ALEU150
ACYS195
AASP196
ALEU197
AASN198
AGLU224
AVAL225
AGLN28
ASER226
AHOH837
AHOH843
AHOH1193
AHOH1194
ATHR30
AASN31
ASER34
ALYS38
AARG88
AGLY115
ACYS116

site_idAC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE CIT A 802
ChainResidue
ALYS484
AILE524
APHE525
AEDO696
AHOH907
AHOH1014
AHOH1018
AHOH1020
AHOH1079
AHOH1166
BLYS326

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 696
ChainResidue
ALEU486
ASER487
AHIS488
AHOH718
ACIT802

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 697
ChainResidue
AGLY615
ALEU655
AHOH755
AHOH933
AHOH1227

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 698
ChainResidue
AVAL438
AASP469
AHOH768
BVAL438
BASP469
BHOH717

site_idAC6
Number of Residues20
DetailsBINDING SITE FOR RESIDUE SAH B 801
ChainResidue
BSER34
BILE35
BLYS38
BARG88
BGLY115
BCYS116
BGLY117
BASP146
BTYR147
BCYS195
BASP196
BLEU197
BASN198
BGLU224
BVAL225
BSER226
BHOH719
BHOH888
BHOH951
BHOH1122

site_idAC7
Number of Residues11
DetailsBINDING SITE FOR RESIDUE CIT B 802
ChainResidue
BLYS484
BILE524
BPHE525
BEDO696
BHOH763
BHOH796
BHOH814
BHOH891
BHOH974
BHOH1159
BHOH1309

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 696
ChainResidue
BLEU486
BSER487
BHIS488
BHOH716
BCIT802

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 697
ChainResidue
BPRO264
BGLY615
BMET654
BLEU655
BHOH726
BHOH918
BHOH1072

site_idBC1
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO B 698
ChainResidue
BHOH794
BHOH866
BHOH876
BHOH1419
BASP392
BHIS443
BHIS493
BGLN601
BHOH776

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton donor; for both methylation and methoxycarbonylation activities => ECO:0000269|PubMed:19287006
ChainResidueDetails
AARG88
BARG88

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: Proton acceptor; for methoxycarbonylation activity => ECO:0000305|PubMed:19287006
ChainResidueDetails
ATYR229
BTYR229

site_idSWS_FT_FI3
Number of Residues12
DetailsBINDING:
ChainResidueDetails
ALYS38
BASP146
BASP196
BGLU224
AARG88
AGLY115
AASP146
AASP196
AGLU224
BLYS38
BARG88
BGLY115

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PDB entries from 2024-07-17

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