1ZE1 | pdb_00001ze1

Conformational Change of Pseudouridine 55 Synthase upon Its Association with RNA Substrate

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1ze1a1 All beta proteins PUA domain-like PUA domain-like PUA domain Pseudouridine synthase II TruB, C-terminal domain (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Ad1ze1a2 Alpha and beta proteins (a+b) Pseudouridine synthase Pseudouridine synthase Pseudouridine synthase II TruB Pseudouridine synthase II TruB (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Dd1ze1d1 All beta proteins PUA domain-like PUA domain-like PUA domain Pseudouridine synthase II TruB, C-terminal domain (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Dd1ze1d2 Alpha and beta proteins (a+b) Pseudouridine synthase Pseudouridine synthase Pseudouridine synthase II TruB Pseudouridine synthase II TruB (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Cd1ze1c1 All beta proteins PUA domain-like PUA domain-like PUA domain Pseudouridine synthase II TruB, C-terminal domain (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Cd1ze1c2 Alpha and beta proteins (a+b) Pseudouridine synthase Pseudouridine synthase Pseudouridine synthase II TruB Pseudouridine synthase II TruB (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Bd1ze1b1 All beta proteins PUA domain-like PUA domain-like PUA domain Pseudouridine synthase II TruB, C-terminal domain (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)
Bd1ze1b2 Alpha and beta proteins (a+b) Pseudouridine synthase Pseudouridine synthase Pseudouridine synthase II TruB Pseudouridine synthase II TruB (Thermotoga maritima ) [TaxId: 2336 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyPUA domain-like 8040283 3001015 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyPseudouridine synthase 8040284 3001360 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyPUA domain-like 8040283 3001015 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyPseudouridine synthase 8040284 3001360 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyPseudouridine synthase 8040284 3001360 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyPUA domain-like 8040283 3001015 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyPUA domain-like 8040283 3001015 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyPseudouridine synthase 8040284 3001360 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APeptidase_S46, Trypsin_2e1ze1A1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: LigT-relatedT: LigT-relatedF: Peptidase_S46, Trypsin_2ECOD (v294.1)
AGATase_2e1ze1A2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: General secretion pathway protein M (EpsM) periplasmic domain-relatedT: General secretion pathway protein M (EpsM) periplasmic domain-relatedF: GATase_2ECOD (v294.1)
DPeptidase_S46, Trypsin_2e1ze1D1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: LigT-relatedT: LigT-relatedF: Peptidase_S46, Trypsin_2ECOD (v294.1)
DGATase_2e1ze1D2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: General secretion pathway protein M (EpsM) periplasmic domain-relatedT: General secretion pathway protein M (EpsM) periplasmic domain-relatedF: GATase_2ECOD (v294.1)
CPeptidase_S46, Trypsin_2e1ze1C1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: LigT-relatedT: LigT-relatedF: Peptidase_S46, Trypsin_2ECOD (v294.1)
CGATase_2e1ze1C2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: General secretion pathway protein M (EpsM) periplasmic domain-relatedT: General secretion pathway protein M (EpsM) periplasmic domain-relatedF: GATase_2ECOD (v294.1)
BPeptidase_S46, Trypsin_2e1ze1B1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: LigT-relatedT: LigT-relatedF: Peptidase_S46, Trypsin_2ECOD (v294.1)
BGATase_2e1ze1B2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: General secretion pathway protein M (EpsM) periplasmic domain-relatedT: General secretion pathway protein M (EpsM) periplasmic domain-relatedF: GATase_2ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthaseCATH (4.3.0)
A2.30.130.10 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase Chain: A, domain 4CATH (4.3.0)
D3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthaseCATH (4.3.0)
D2.30.130.10 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase Chain: A, domain 4CATH (4.3.0)
C3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthaseCATH (4.3.0)
C2.30.130.10 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase Chain: A, domain 4CATH (4.3.0)
B3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthaseCATH (4.3.0)
B2.30.130.10 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase Chain: A, domain 4CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D
PF16198tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)tRNA pseudouridylate synthase B C-terminal domain- Family
A, B, C, D
PF01509TruB family pseudouridylate synthase (N terminal domain) (TruB_N)TruB family pseudouridylate synthase (N terminal domain)Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in m ...Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA [2].
Domain
A, B, C, D
PF01472PUA domain (PUA)PUA domainThe PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modificatio ...The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes [1]. It is predicted that the PUA domain is an RNA binding domain.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D
tRNA pseudouridine synthase B -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D
IPR015947PUA-like superfamilyHomologous Superfamily
A, B, C, D
IPR020103Pseudouridine synthase, catalytic domain superfamilyHomologous Superfamily
A, B, C, D
IPR002501Pseudouridine synthase II, N-terminalDomain
A, B, C, D
IPR032819tRNA pseudouridylate synthase B, C-terminalDomain
A, B, C, D
IPR036974PUA domain superfamilyHomologous Superfamily
A, B, C, D
IPR014780tRNA pseudouridine synthase II, TruBFamily
A, B, C, D
IPR002478PUA domainDomain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
tRNA-pseudouridine synthase  M-CSA #56

tRNA-pseudouridine synthase II (TruB) from Thermotoga maritima catalyses the conversion of tRNA uridine to tRNA pseudouridine at position 55 in tRNA. The formation of pseudouridine is shown to be important for the structural integrity of tRNA.

TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA [PMID:11779468].

The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. [PMID:10529181]

There is still much debate as to the exact mechanism of this enzyme.

Defined by 4 residues: ASP:A-39TYR:A-67ASP:A-81ARG:A-172
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Explore in 3D: M-CSA Motif Definition
Search M-CSA Motif
EC: 4.2.1.70 (PDB Primary Data)
EC: 5.4.99.25 (UniProt)