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Record W2071766792 · doi:10.1074/jbc.m510522200

Crystallographic Trapping of the Glutamyl-CoA Thioester Intermediate of Family I CoA Transferases

2005· article· en· W2071766792 on OpenAlexafffund
Erumbi S. Rangarajan, Yunge Li, Eunice Ajamian, P. Iannuzzi, S.D. Kernaghan, M.E. Fraser, Mirosław Cygler, Allan Matte

Bibliographic record

VenueJournal of Biological Chemistry · 2005
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicMetabolism and Genetic Disorders
Canadian institutionsUniversity of CalgaryBiotechnology Research InstituteMcGill University
FundersBiological and Environmental ResearchBasic Energy SciencesNational Center for Research ResourcesCanadian Institutes of Health ResearchNational Institutes of HealthFondation pour la Recherche MédicaleU.S. Department of Energy
KeywordsTransferaseThioesterCoenzyme AEscherichia coliAcyl-CoAAcyl carrier proteinBiochemistryChemistryProtein structureCofactorSubstrate (aquarium)StereochemistryBiologyEnzymeCrystallographyGene

Abstract

fetched live from OpenAlex

Coenzyme A transferases are involved in a broad range of biochemical processes in both prokaryotes and eukaryotes, and exhibit a diverse range of substrate specificities. The YdiF protein from Escherichia coli O157:H7 is an acyl-CoA transferase of unknown physiological function, and belongs to a large sequence family of CoA transferases, present in bacteria to humans, which utilize oxoacids as acceptors. In vitro measurements showed that YdiF displays enzymatic activity The of YdiF and CoA and and YdiF is an of CoA of YdiF a of CoA in of in a The CoA a and The of YdiF a in of CoA Coenzyme A transferases are involved in a broad range of biochemical processes in both prokaryotes and eukaryotes, and exhibit a diverse range of substrate specificities. The YdiF protein from Escherichia coli O157:H7 is an acyl-CoA transferase of unknown physiological function, and belongs to a large sequence family of CoA transferases, present in bacteria to humans, which utilize oxoacids as acceptors. In vitro measurements showed that YdiF displays enzymatic activity The of YdiF and CoA and and YdiF is an of CoA of YdiF a of CoA in of in a The CoA a and The of YdiF a in of CoA Coenzyme A is a as as of a diverse of and and and of an from substrate to as of an enzymatic that A is in CoA as an and is and as a in CoA transferases, which of CoA from a CoA to a and a acyl-CoA to of large of CoA transferases, CoA CoA as in in and of CoA transferases and sequence as a and a The of CoA transferases is of and a and are both and from of an and of CoA transferases are to substrate of biochemical and are of and a of substrate an to that and CoA of acyl-CoA substrate to The of CoA as are CoA transferases, CoA transferase from transferase from Escherichia coli and from substrate The of an CoA transferase a of present of YdiF and to of CoA measurements in vitro that YdiF is a CoA transferase and as broad substrate acyl-CoA activity of CoA in of an to of a to involved in substrate and a in and from coli O157:H7 and The a and in coli as a a The coli of protein in protein a in and of The and protein of in The of and and YdiF The protein in and to The protein in a a an YdiF to and protein of measurements a a protein of in and an YdiF protein to in and The of YdiF in a of and CoA in and of of of and in of YdiF enzymatic activity to A A of and of YdiF and and of A and of transferase from as a from The YdiF of protein in of and of to a of in to a in a and in a of YdiF to a and a of and a of of of YdiF and and of YdiF in and of in a and a to a and in in of and to a and from and a and and from a YdiF a a and in to and to a of of of of and of of and of of The from of and of a from from a from from in a The and and in The of of and The and an of and of to YdiF CoA a as and The of as of of showed in from and which showed to and of CoA In of from is of to a of of CoA from and an of of from are in an is in A transferase diverse substrate coli and of YdiF are in sequence to and and of The to a CoA transferase an is transferase from which sequence YdiF to that YdiF YdiF sequence to from The and of YdiF and and of CoA transferases exhibit a broad activity CoA and acyl-CoA in vitro activity CoA activity as an as YdiF and as CoA CoA in of activity of YdiF CoA that of activity and sequence that YdiF a in in coli Escherichia coli and vitro activity of activity to activity to in a YdiF of a and YdiF of an and an A The is of a of are a and a The of is of and a The a a and a and and a The to a a and of are in and of and and of of YdiF and and The is in YdiF that and and an The and a of sequence of in The of sequence that in A and of which in as both and The that YdiF is as a of The are involved in a of of of The of in of The of a are that substrate of of both and of protein and are of and in of to The as a of is to of The a of to that a of involved YdiF and in and involved in are Coenzyme substrate and involved in YdiF A in of in of CoA in of The of CoA in from In of YdiF to that of a and CoA in and In showed that In both as as and a In YdiF in A and and of to in and In to from The CoA and to of of CoA The is a in of and CoA from The YdiF and CoA are in The CoA is an and and of CoA in and and of and of and CoA a of that CoA large of CoA protein is which is to of and to of and to of and of and of and The of is to of to of and a to of and of and The a of The of and A is and of a of and of CoA of and of of of in of YdiF a to a of which is in of of to The to of of CoA and of as of that in of as and enzymatic CoA transferases, sequence and are sequence and In that of is of a to of In is that a of of In of is involved in a CoA a and a to of In a in and is to a to and of of and in of in of that in YdiF in and of in YdiF and of CoA from and of of YdiF and and of to YdiF CoA of YdiF of and of and a of in YdiF and are is of a in of a are transferase in a and a The and are of and In is in and A of is present in and In YdiF an and a that is in CoA of YdiF and that of involved CoA in to of of and of are in of both and to exhibit CoA as that an to as are of CoA transferases that are involved in of of and that to involved in In and and to in in are of and are in The in YdiF in and to in in and in of of CoA transferases, of A from acyl-CoA to in a of a A and The in and to of In of in of CoA and of a In of CoA of in a and of In of of CoA from and a In of CoA of and an in and to CoA transferases The and as as CoA are of is that and a in CoA transferase The of is to in of in a of The to of YdiF in and in In of YdiF of is in in which a CoA and in which in of In of to an The of from that in a of is in in displays in which to in YdiF is involved in in acyl-CoA is of a The of from to as a in of and in in that of of CoA in of to of is of of of of CoA transferases is of from to an a in of of to of an and in YdiF to in The a to of of in of of from to as as of and of of CoA of and of from to The are an of of an CoA transferases and to of that of CoA in an of in In of of CoA to in both and and in The of of CoA as to is present that of CoA is and that of In of are a which of of in CoA of and CoA to of CoA in of CoA are are in is from that that and and to of in of and The of of an in and is to in of CoA Coenzyme A is a as as of a diverse of and and and of an from substrate to as of an enzymatic that A is in CoA as an and is and as a in CoA transferases, which of CoA from a CoA to a and a acyl-CoA to of large of CoA transferases, CoA CoA as in in and CoA transferase CoA transferase of CoA transferases and sequence as a and a The of CoA transferases is of and a and are both and from of an and of CoA transferases are to substrate A of biochemical and are of and a of substrate an to that and CoA of acyl-CoA substrate to The of CoA as are CoA transferases, CoA transferase from transferase from Escherichia coli and from substrate The of an CoA transferase a of present of YdiF and to of CoA measurements in vitro that YdiF is a CoA transferase and as broad substrate acyl-CoA activity of CoA in of an to of a to involved in substrate and a in and from coli O157:H7 and The a and in coli as a a The coli of protein in protein a in and of The and protein of in The of and and YdiF The protein in and to The protein in a a an YdiF to and protein of measurements a a protein of in and an YdiF protein to in and The of YdiF in a of and CoA in and of of of and in of YdiF enzymatic activity to A A of and of YdiF and and of A and of transferase from as a from The YdiF of protein in of and of to a of in to a in a and in a of YdiF to a and a of and a of of of YdiF and and of YdiF in and of in a and a to a and in in of and to a and from and a and and from a YdiF a a and in to and to a of of of of and of of and of of The from of and of a from from a from from in a The and and in The of of and The and an of and of to YdiF CoA a as and The of as of of showed in from and which showed to and of CoA In of from is of to a of of CoA from and an of of from are in and from coli O157:H7 and The a and in coli as a a The coli of protein in protein a in and of The and protein of in The of and and YdiF The protein in and to The protein in a a an YdiF to and protein of measurements a a protein of in and an YdiF protein to in and The of YdiF in a of and CoA in and of of of and in of YdiF enzymatic activity to A A of and of YdiF and and of A and of transferase from as a from The YdiF of protein in of and of to a of in to a in a and in a of YdiF to a and a of and a of of of YdiF and and of YdiF in and of in a and a to a and in in of and to a and from and a and and from a YdiF a a and in to and to a of of of of and of of and of of The from of and of a The and and in The of of and The and an of and of to YdiF CoA a as and The of as of of showed in from and which showed to and of CoA In of from is of to a of of CoA from and an of of from are in an is in A transferase diverse substrate coli and of YdiF are in sequence to and and of The to a CoA transferase an is transferase from which sequence YdiF to that YdiF YdiF sequence to from The and of YdiF and and of CoA transferases exhibit a broad activity CoA and acyl-CoA in vitro activity CoA activity as an as YdiF and as CoA CoA in of activity of YdiF CoA that of activity and sequence that YdiF a in in coli Escherichia coli and vitro activity of activity to activity to in a YdiF of a and YdiF of an and an A The is of a of are a and a The of is of and a The a a and a and and a The to a a and of are in and of and and of an The and a of sequence of in The of sequence that in A and of which in as both and The that YdiF is as a of The are involved in a of of of The of in of The of a are that substrate of of both and of protein and are of and in of to The as a of is to of The a of to that a of involved YdiF and in and involved in are Coenzyme substrate and involved in YdiF A in of in of CoA in of The of CoA in from In of YdiF to that of a and CoA in and In showed that In both as as and a In YdiF in A and and of to in and In to from The CoA and to of of CoA The is a in of and CoA from The YdiF and CoA are in The CoA is an and and of CoA in and and of and of and CoA a of that CoA large of CoA protein is which is to of and to of and to of and of and of and The of is to of to of and a to of and of and The a of The of and A is and of a of and of CoA of and of of of in of YdiF a to a of which is in of of to The to of of CoA and of as of that in of as and enzymatic CoA transferases, sequence and are sequence and In that of is of a to of In is that a of of In of is involved in a CoA a and a to of In a in and is to a to and of of and in of in of that in YdiF in and of in YdiF and of CoA from and of of YdiF and and of to YdiF CoA of YdiF of and of and a of in YdiF and are is of a in of a are transferase in a and a The and are of and In is in and A of is present in and In YdiF an and a that is in CoA of YdiF and that of involved CoA in to of of and of are in of both and to exhibit CoA as that an to as are of CoA transferases that are involved in of of and that to involved in In and and to in in are of and are in The in YdiF in and to in in and in of of CoA transferases, of A from acyl-CoA to in a of a A and The in and to of In of in of CoA and of a In of CoA of in a and of In of of CoA from and a In of CoA of and an in and to CoA transferases The and as as CoA are of is that and a in CoA transferase The of is to in of in a of The to of YdiF in and in In of YdiF of is in in which a CoA and in which in of In of to an The of from that in a of is in in displays in which to in YdiF is involved in in acyl-CoA is of a The of from to as a in of and in in that of of CoA in of to of is of of of of CoA transferases is of from to an a in of of to of an and in YdiF to in The a to of of in of of from to as as of and of of CoA of and of from to The are an of of an CoA transferases and to of that of CoA in an of in In of of CoA to in both and and in The of of CoA as to is present that of CoA is and that of In of are a which of of in CoA of and CoA to of CoA in of CoA are are in is from that that and and to of in of and The of of an in and is to in of CoA YdiF an is in A transferase diverse substrate coli and of YdiF are in sequence to and and of The to a CoA transferase an is transferase from which sequence YdiF to that YdiF YdiF sequence to from The and of YdiF and and of CoA transferases exhibit a broad activity CoA and acyl-CoA in vitro activity CoA activity as an as YdiF and as CoA CoA in of activity of YdiF CoA that of activity and sequence that YdiF a in in coli Escherichia coli and vitro activity of activity to activity to in a YdiF is in A transferase diverse substrate coli and of YdiF are in sequence to and and of The to a CoA transferase an is transferase from which sequence YdiF to that YdiF YdiF sequence to from The and of YdiF and and of CoA transferases exhibit a broad activity CoA and acyl-CoA in vitro activity CoA activity as an as YdiF and as CoA CoA in of activity of YdiF CoA that of activity and sequence that YdiF a in in coli Escherichia coli and YdiF of a and YdiF of an and an A The is of a of are a and a The of is of and a The a a and a and and a The to a a and of are in and of and and of an The and a of sequence of in The of sequence that in A and of which The YdiF of a and YdiF of an and an A The is of a of are a and a The of is of and a The a a and a and and a The to a a and of are in and of and and of The an The and a of sequence of in The of sequence that in A and of which in as both and The that YdiF is as a of The are involved in a of of of The of in of The of a are that substrate of of both and of protein and are of and in of to The as a of is to of The a of to that a of involved YdiF and in and involved in are YdiF in as both and The that YdiF is as a of The are involved in a of of of The of in of The of a are that substrate of of both and of protein and are of and in of to The as a of is to of The a of to that a of involved YdiF and in and involved in are Coenzyme substrate and involved in YdiF A in of in of CoA in of The of CoA in from In of YdiF to that of a and CoA in and In showed that In both as as and a In YdiF in A and and of to in and In in of and CoA from The YdiF and CoA are in The CoA is an and and of CoA in and and of and of and CoA a of that CoA large of CoA protein is which is to of and to of and to of and of and of and The of is to of to of and a to of and of and The a of The of and A is and of a of and of CoA of and of of of in of YdiF a to a of which is in of of to The to of of CoA and of as of that in of as and enzymatic substrate and involved in YdiF A in of in of CoA in of The of CoA in from In of YdiF to that of a and CoA in and In showed that In both as as and a In YdiF in A and and of to in and In CoA in of and CoA from The YdiF and CoA are in The CoA is an and and of CoA in and and of and of and CoA a of that CoA large The of CoA protein is which is to of and to of and to of and of and of and The of is to of to of and a to of and of and The a of The of and A is and of a of and of CoA of and of of of in of YdiF a to a of which is in of of to The to of of CoA and of as of that in of as and enzymatic CoA transferases, sequence and are sequence and In that of is of a to of In is that a of of In of is involved in a CoA a and a to of In a in and is to a to and of of and in of in of that in YdiF In CoA transferases, sequence and are sequence and In that of is of a to of In is that a of of In of is involved in a CoA a and a to of In a in and is to a to and of of and in of in of that in YdiF CoA of YdiF of and of and a of in YdiF and are is of a in of a are transferase in a and a The and are of and In is in and A of is present in and In YdiF an and a that is in CoA of YdiF and that of involved CoA in to of of and of are in of both and to exhibit CoA as that an to as are of CoA transferases that are involved in of of and that to involved in In and and to in in are of and are in The in YdiF in and to in in and in of of CoA transferases, of A from acyl-CoA to in a of a A and The in and to of In of in of CoA and of a In of CoA of in a and of In of of CoA from and a In of CoA of and an in of is that and a in CoA transferase The of is to in of in a of The to of YdiF in and in In of YdiF of is in in which a CoA and in which in of In of to an The of from that in a of is in in displays in which to in YdiF is involved in in acyl-CoA is of a The of from to as a in of and in in that of of CoA in of to of is of of of of CoA transferases is of from to an a in of of to of an and in YdiF to in The a to of of in of of from to as as of and of of CoA of and of from to The are an of of an CoA transferases and to of that of CoA in an of in In of of CoA to in both and and in The of of CoA as to is present that of CoA is and that of In of are a which of of in of YdiF of and of and a of in YdiF and are is of a in of a are transferase in a and a The and are of and In is in and A of is present in and In YdiF an and a that is in CoA CoA of YdiF and that of involved CoA in to of of and of are in of both and to exhibit CoA as that an to as are of CoA transferases that are involved in of of and that to involved in In and and to in in are of and are in The in YdiF in and to in in and in of of CoA transferases, of A from acyl-CoA to in a of a A and The in and to of In of in of CoA and of a In of CoA of in a and of In of of CoA from and a In of CoA of and an in of is that and a in CoA transferase The of is to in of in a of The to of YdiF in and in In of YdiF of is in in which a CoA and in which in of In of to an The of from that in a of is in in displays in which to in YdiF is involved in in acyl-CoA is of a The of from to as a in of and in in that of of CoA in of to of is of of of of CoA transferases is of from to an a in of of to of an and in YdiF to in The a to of of in of of from to as as of and of of CoA of and of from to The are an of of an CoA transferases and to of that of CoA in an of in In of of CoA to in both and and in The of of CoA as to is present that of CoA is and that of In of are a which of of in CoA of and CoA to of CoA in of CoA are are in is from that that and and to of in of and The of of an in and is to in of CoA In CoA of and CoA to of CoA in of CoA are are in is from that that and and to of in of and The of of an in and is to in of CoA

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.027
Threshold uncertainty score0.359

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.016
GPT teacher head0.239
Teacher spread0.223 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one teacher head, not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

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Citations43
Published2005
Admission routes2
Has abstractyes

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