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Table 2 Annotation of uncharacterized proteins based on our ligand-centric approach

From: Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

PDB ID

CURRENT ANNOTATION IN PDB

PIRSF ID

TAXONOMY

PREDICTED LIGAND CONFORMATION & CLASS

SUGGESTED NAME

2PGX

Crystal structure of UPF0341 protein yhiQ from E. coli

SF016106

E=0, B=156, A=0, V=0, O=4

Type 1

Putative SAM dependent r-RNA methyltransferase

Class 1a

2O3A

Crystal structure of a protein AF_0751 from Archaeoglobus fulgidus

SF016123

E=0, B=0, A=134, V=0, O=0

Type IV

Putative SAM dependent t-RNA archaeal methyltransferase

Class IV

2B78

A putative sam-dependent methyltransferase from Streptococcus mutans

SF004981

E=2, B=403, A=16, V=0, O=5

Type 1

Putative SAM dependent RNA methyltransferase

Class 1a

3DR5

Crystal structure of the Q8NRD3_CORGL protein from Corynebacterium glutamicum

SF005841

E=122, B=346, A=6, V=0, O=3

Type 1

Putative SAM dependent COMT type methyltransferase

Class 1b

1XXL

The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A resolution

SF006616

E=6, B=130, A=2, V=0, O=4

Type 1

Putative SAM dependent Class Ib methyltransferase

Class 1b

1YB2

Structure of a putative methyltransferase from Thermoplasma acidophilum

SF017269

E=227, B=418, A=110, V=0, O=2

Type 1

Putative SAM dependent t-RNA methyltransferase

Class 1a

1JSX

Crystal Structure of the Escherichia coli Glucose-Inhibited Division Protein B (GidB)

SF003078

E=19, B=4040, A=0, V=0, O=13

Type 1

Putative SAM dependent r-RNA methyltransferase

    

Class 1b

 
  1. Functions are assigned based on the results of the analysis presented in this manuscript. Majority of the structures are from Structural Genomics Initiatives with unassigned functions.