Supplementary material for Evolutionary history and higher
order classification of AAA+ ATPases
Lakshminarayan M. Iyer, Detlef D. Leipe, Eugene V. Koonin and
L. Aravind, Journal of Structural Biology
SR[CAT] motif associated with Arginine finger
*HolB/DNAX family
Zn cluster between Helix-1 and
* * Hol B subfamily [B]
* * DNAX
subfamily [B, Pl]
*RFC family
* *MTH241/RFC2 subfamily [AE]
(In eukaryotes includes RFC2,
RFC3, RFC4, RFC5)
*
*MTH240/RFC1 subfamily [AE]
(In eukaryotes includes RFC1, Chl12,
RAD24, Yor144c)
Fused to a C-terminal WC domain
DnaA/ORC clade
Two
helices of approximately equal length after strand 2
*DnaA family
* *DnaA subfamily
[B]
* *DnaC subfamily
[B]
* * CDC6/ORC [A]
* * Orc1p, Orc4p, Orc5p and Cdc6p subfamilies [E]
Classical AAA clade
and its divergent relatives
Small
helix between Strand-2 and Helix-3, [GN]R motif associated with arginine finger
Fused to a metalloprotease at the
C-terminus.
* CDC48 family [A, E]
DPBB at N-terminus, 2 AAA+ domains
* Proteasomal ATPase family [A, E]
*
* S4, S6a, S6b, S7, S8, S10a and S10b subfamilies
[E]
*Katanin p60/Fidgetin
family [E]
*NSF1
family [E]
*Pex1/6
subfamily [E]
* Bcs1p
subfamily [E]
(Possible relatives
of classical AAA clade)
*AFG1 family [B, E]
*ClpAB-N family
[B>A, E]
*TIP49 family [A, E]
N-terminal module with characteristic H[ST]H
motif, Predicted b
barrel
between Helix-3 and
b- hairpin inserted before Sensor 1 motif
SFIII
helicase clade [viruses]
* NCLDV
D5 ATPase family
* Positive strand RNA virus helicase family
* Other viral helicases
Extended loop after strand 2
*HslU/ClpX family
* *HslU subfamily [B, Kin,
Api]
* *ClpX subfamily [B, E]
*Lon family
Fused
to a Lon protease at the C-terminus
* *Bacterial lon protease subfamily [B, E]
Fused to a LAN domain at the N-terminus
* *Archaeal lon protease subfamily [A>B]
*ClpAB-C family
NRhD
motif associated with Arginine finger
* *ClpAB-C subfamily [B, E]
*
*Torsin subfamily [E]
Torsin has a distinct a
helical N-terminal domain
Has C-terminal wHTH domain; Helical segment
between strand 5 and C-terminal bundle
Helix-2 insert clade
b-a-b insert in helix 2
NtrC/MCM group
Have
[AG][FL]T motif in helix 2 before b-a-b insert
* NtrC family [B]
Fused to a Zn ribbon at N-terminus and a
wHTH at the C-terminus
* *Chelatase family [A, B, plants]
Associated with a vWA domain
* * YifB family [B]
Fused to a Lon
Protease at its N-terminus, insert of Zn cluster after strand 4
* * MoxR family [A, B]
* *Dynein/Midasin family
6 Tandem AAA+ domains
* *Dynein subfamily [E]
* *Midasin subfamily [E]