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Table 2 Summary of differences in DNA replication machinery of Archaea and Bacteria.

From: The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

Function

Superkingdom

Protein

PDB ID (if applicable)

SCOP Superfamily Combination

Proposed Origin in Archaea

Origin recognition

Bacteria

DnaA

1l8q

_gap_,52540,48295

 
 

Archaea

Cdc6/ORC (single or multiple homologues)

1fnn

52540, 46785

evolved from RuvB

Replicative helicase

Bacteria

DnaC

3ec2

52540 *

 
 

Archaea

MCM

3f9v

 

viral transfer

Helicase loader

Bacteria

DnaB

1b79 (n-terminal domain)

gap, 48024

 

ssDNA-binding protein

Archaea, Bacteria

SSB (one subunit)

1o7i

50249

archaeal SSB evolved from bacterial SSB

 

Archaea

RPA (one or three subunits)

2b28

50249, 50249, 50249

evolved from SSB

Primase

Bacteria

DnaG

1dd9

56731

 
 

Archaea

PriA (small)

1zt2:a

56747, gap

viral transfer or vertically inherited

 

Archaea

PriB(large)

1zt2:b

140914

innovation

Replicative Polymerase

Archaea, Bacteria

PolB (one or multiple homologues)

1q8i

gap, 56672

viral transfer

 

Archaea

PolD (small)

none

gap, 56300

innovation

 

Archaea

PolD (large)

none

gap

innovation

 

Bacteria

PolC (DnaE)

2hqa

89550, large gap*

 

DNA sliding clamp

Archaea

PCNA (three subunits)

3a2f

55979, 55979

evolved from β-clamp

 

Bacteria

β-clamp (dimer)

1ok7

55979, 55979, 55979

 

Clamp loader

Bacteria

γ-Complex (three subunits)

1jr3:a

52540, 48019

 
 

Archaea

RFC (two subunits)

1iqp

52540, 48019

evolved from γ-Complex

Removal of primers

Archaea

Fen1

1rxw

88723, 47807

viral origin

 

Bacteria

RNase H

1jl1

53098

 
 

Archaea

RNase HII

1eke

53098

archaeal RNAase HII evolved from bacterial RNAase HI

 

Bacteria

PolA

2kfz (mssing c-terminal domain)

53098, 56672

 
 

Archaea, Bacteria

DNA ligase(ATP-DEP)

1xn9 (human)

117018, 56091, 50249

viral origin or vertical inheritance

 

Bacteria

DNA ligase(NAD-DEP)

1dgs

56091, 50249, 47781

 

Preinitiation complex

Archaea

gins

2eho(human)

158573

true innovation

  1. The list of protein functions was compiled from box 1 in [20] and table one in [129]. Italics indicate a probable horizontal transfer to a superkingdom. There are very few proteins in archaea that are true innovations. Many of their unique replication proteins could be recruited from bacterial or viral systems. A * indicates the Superfamily database was used to predict domain assignments of PDB entries not yet classified in SCOP.