P-type ATPase superfamily: Tables

Table 1.
P-type ATPases included in the phylogenetic analysis
Number useda Accession numberb Organism Specificityc Name
Type IA ATPases
20 P03960 Escherichia coli K+ kdpB / f682
21 Z92539
 Mycobacterium tuberculosis
kdpB
22 D90910 Synechocystis PCC6803
kdpB / slr1729
Type IB ATPases
23 U78967 Lactococcus lactis
cadA
24 L28104 Listeria monocytogenes Cd2+ cadA
25 P30336 Bacillus firmus
cadA
26 P37386 Staphylococcus aureus
cadD
27 D64005 S. PCC6803
cadA_2 / slr0798
28 D64005 S. PCC6803
cadA_1 / slr0797
29 L46864 Helicobacter pylori

30 Q10866 M. tuberculosis
MTCY39.27
31 P37617 E. coli
yhh0 / o732
32 Z92771 M. tuberculosis
MTCY71.10
33 P77871 H. pylori Cu2+ copA
34 U32715 Haemophilus influenzae
hi290
35 Q59385 E. coli
f834
36 P05425 Enterococcus hirae Cu2+ copB
37 P37385 Synechococcus PCC7942 Cu2+ synA
38 D90915 S. PCC6803
slr1950
39 Z79700 M. tuberculosis
MTCY10D7.05c
40 P46840 Mycobacterium leprae
ctpB
41 Q10876 M. tuberculosis
ctpA / MTCY251.11
42 Q10877 M. tuberculosis
ctpB / MTCY251.22c
43 P46839 M. leprae
ctpA
44 U42410 Proteus mirabilis

45 D90904 S. PCC6803
sll1920
46 P37279 S. PCC7942 Cu2+ pacS
47 U15554 L. monocytogenes Cu2+ ctpA
48 P38995 Saccharomyces cerevisiae Cu2+ CCC2 / ydr270w
49 Q04656 Homo sapiens Cu2+ ATP7A / MNK
50 U08344 Rattus norvegicus Cu2+ ATP7B
51 P35670 H. sapiens Cu2+ ATP7B / WND
52 P38360 S. cerevisiae
PCA1 / ybr295w
53 X95634 Bradyrhizobium japonicum
fixI
54 P18398 Rhizobium meliloti
fixI
55 U16659 Unknown d
hra2
56 P32113 E. hirae Cu2+ copA
57 U16658 Unknown d
hra1
Type IIA ATPases
130 Q10860 M. tuberculosis
MTCY39.21c
131 P37367 S. PCC6803
pma1 / sll1614
132 M93017 R. norvegicus

133 P13586 S. cerevisiae Ca2+ PMR1
134 U65981 Cryptosporidium parvum
CppA-E1
135 U39298 Plasmodium falciparum
PfATPase4
136 U65066 Trichomonas vaginalis
TVCA1
137 P54209 Dunaliella bioculata
CA1
138 U70540 Leishmania mexicana amazonensis

139 P35315 Trypanosoma brucei
TBA1
140 L40328 Schistosoma mansoni
SMA1
141 P16615 H. sapiens Ca2+ ATP2A2 / SERCA2
142 U65228 Makaira nigricans
SERCA1A
143 X63009 Rana esculenta Ca2+
144 M99223 R. norvegicus Ca2+
145 P18596 R. norvegicus Ca2+ ATP2A3 / SERCA3
146 P22700 Drosophila melanogaster
DRSERCA / CA-60A
147 P35316 Artemia franciscana

148 Q08853 P. falciparum

149 X55197 Plasmodium yoelii
YEL6
150 M96324 Lycopersicon esculentum
LCA1
151 U82966 Oryza sativa

152 U93845 Arabidopsis thaliana
ACA3
153 D64005 S. PCC6803
pacL / sll0672
154 P37278 S. PCC7942
pacL
155 D90911 S. PCC6803
pacL / slr0822
Type IIB ATPases
118 U05880 Paramecium tetraurelia

119 X99972 Brassica oleracea Ca2+ BCA1
120 L08468 A. thaliana
PEA1
121 U20321 e Entamoeba histolytica

122 U15408 R. norvegicus

123 P23634 H. sapiens Ca2+ ATP2B4 / PMCA4
124 P20020 H. sapiens Ca2+ ATP2B1 / PMCA1
125 Q16720 H. sapiens Ca2+ ATP2B3 / PMCA3
126 Q01814 H. sapiens Ca2+ ATP2B2 / PMCA2
127 Z68221 Caenorhabditis elegans

128 P54678 Dictyostelium discoideum
patA
129 P38929 S. cerevisiae Ca2+ PMC1 / ygl006w
Type IIC ATPases
97 U70316 f D. discoideum
IonA
98 Z81457 g C. elegans

99 P35317 Hydra vulgaris Na+/K+
100 P28774 A. franciscana

101 U18546 C. elegans Na+/K+ eat-6
102 P13607 D. melanogaster Na+/K+ NA-P
103 S66043 Ctenocephalides felis

104 P05023 H. sapiens Na+/K+ ATP1A1 / NaKalpha1
105 P05025 Torpedo californica Na+/K+ ATP1A1 / NaKalpha1
106 P13637 H. sapiens Na+/K+ ATP1A3 / NaKalpha3
107 Q92030 Anguilla anguilla

108 P25489 Catostomus commersoni

109 P50993 H. sapiens Na+/K+ ATP1A2 / NaKalpha2
110 U15176 R. norvegicus
ATP1A4 / NaKalpha4
111 P17326 A. franciscana Na+/K+
112 P20648 H. sapiens H+/K+ ATP4A
113 U17249 Xenopus laevis H+/K+
114 D21854 Cavia cobaya

115 P54707 H. sapiens H+/K+ ATP1AL1
116 P54708 R. norvegicus H+/K+ ATP1AL1
117 Z25809 Bufo marinus H+/K+
Type IID ATPases
93 P22189 Schizosaccharomyces pombe Ca2+ CTA3
94 P13587 S. cerevisiae Na+ ENA1 / ydr040c
95 D78567 Zygosaccharomyces rouxii
Z-ENA1
Type IIIA ATPases
61 U67563 Methanococcus jannaschii
mj1226
62 P54210 Dunaliella acidophila H+ dha1
63 P54211 D. bioculata
PMA1
64 P54679 D. discoideum

65 D88424 Cyanidium caldarium

66 X76535 Solanum tuberosum
PHA2
67 Q03194 Nicotiana plumbaginifolia
PMA4
68 P19456 A. thaliana H+ AHA2
69 P20431 A. thaliana H+ AHA3
70 S79323 Vicia faba

71 D45189 Zostera marina
ZHA1
72 X85805 Zea mays
MHA2
73 U84891 Mesembryanthemum crystallinum
PMA
74 X73676 A. thaliana
AHA9
75 D31843 O. sativa
OSA2
76 U09989 Z. mays
MHA1
77 D10207 O. sativa
OSA1
78 M27888 N. plumbaginifolia H+ PMA2
79 X85804 Phaseolus vulgaris
BHA1
80 S74033 A. thaliana
AHA10
81 P12522 Leishmania donovani
ATPase1b
82 D26472 Heterosigma akashiwo

83 P24545 Z. rouxii H+
84 P28877 Candida albicans
PMA1
85 P49380 Kluyveromyces lactis
PMA1
86 P05030 S. cerevisiae H+ PMA1 / ygl008c
87 P19657 S. cerevisiae H+ PMA2 / ypl036w
88 U65004 Pneumocystis carinii
PCA1
89 P28876 S. pombe H+ PMA2
90 P09627 S. pombe H+ PMA1
91 P07038 Neurospora crassa H+ PMA1
92 Q07421 Histoplasma capsulatum
PMA1
Type IIIB ATPases
58 P22036 Salmonella typhimurium Mg2+ mgtB
59 P39168 E. coli
mgtA / o898
60 P36640 S. typhimurium Mg2+ mgtA
Type IV ATPases
8 Z81078 C. elegans

9 P40527 S. cerevisiae
yil048w
10 Q10309 S. pombe
SPAC6C3.05C
11 U28940 h C. elegans
T24H7.5
12 U16955 P. falciparum
PfATPase2
13 Q12674 S. cerevisiae
ymr162c
14 U51100 Bos taurus PL
15 P39524 S. cerevisiae PL DRS2 / yal026c
16 Q09891 S. pombe
SPAC24B11.12C
17 Q12675 S. cerevisiae
ydr093w
18 P32660 S. cerevisiae
yer166w
Type V ATPases
1 Q12697 S. cerevisiae
yor291w
2 Z70271 C. elegans
W08D2.5
3 U41552 i C. elegans

4 X65738 P. falciparum
PfATPase1
5 Z83217 C. elegans

6 P39986 S. cerevisiae
yel031w
7 U41063 Tetrahymena thermophila
TPA9
Others
158 Q10900 M. tuberculosis
MTCY251.26C
96 D90905 S. PCC6803
pacL / sll1076
157 P47317 Mycoplasma genitalium
pacL / mg071
159 Z84724 M. tuberculosis
MTCY22G10.22c
19 Z95210 M. tuberculosis
MTCY21C12.02
156 P78036 Mycoplasma pneumoniae
mgtA / G07_872V


Footnotes:
a The number and the groupings refer to the sequence numbers and groups used in all figures
b The accession numbers starting with a Q or P are from the SWISS-PROT database. All other accession numbers are from the EMBL database
c The ion specificity of the P-type ATPases is shown, when it has been experimentally shown. PL: phospholipids
d The sequences were found in a human cDNA library. They were suggested to originate from E. coli, but could not be identified in the genome
e The N-terminus is missing. Sequence alignments with other type IIB ATPases indicate that the sequence is probably 80-130 amino acids longer
f Both termini are missing. Sequence alignments with other type IIC ATPases indicate that the sequence is probably 30-45 amino acids longer
g Only genomic sequence data are available and no proposed translation. The conserved segments have therefore been extracted directly from the genomic clone
h The proposed translation of the genomic DNA sequence lacks the region around the conserved segment D (Fig. 2). The sequence can be corrected by inserting two additional exons from nucleotide 9,394 to 9,573 and from nucleotide 10,127 to 10,223. An expressed sequence tag (D68066) covering this area of the protein further supports the corrections
i The proposed translation of the genomic DNA sequence lacks several of the conserved regions. The conserved segments have therefore been extracted directly from the genomic clone



Table 2.
P-type ATPases, which are excluded from the phylogenetic analysis.

Sequences were excluded if they showed more than 90% identity to other sequences in the dataset.

Accession number a Organism
(Open reading frame)		 ATPase
type		 >90%
identity
with
seq. no.b		 Ion
speci-
ficityc		 Name
P20021 Staphylococcus aureus IB 26 Cd2+ cadA
Q59467 Helicobacter pylori IB 33
copA2
P49015 Cricetulus griseus IB 49
ATP7A
U03434 Mus musculus IB 49 Cu2+ ATP7A / MNK
U59245 Rattus norvegicus IB 49 Cu2+ ATP7A / MNK
U38477 M. musculus IB 51
ATP7B / WND
Z69881 Homo sapiens IIA 145 Ca2+ ATP2A3 / SERCA3
P13585 Gallus gallus IIA 144 Ca2+ ATP2A1 / SERCA1
P04191 Oryctolagus cuniculus IIA 144 Ca2+ ATP2A1 / SERCA1
P11719 O. cuniculus IIA 144 Ca2+ ATP2A1 / SERCA1
P16614 H. sapiens IIA 141 Ca2+ ATP2A2 / SERCA2
Q00779 Felis silvestris catus IIA 141 Ca2+ ATP2A2 / SERCA2
M66385 G. gallus IIA 141 Ca2+ ATP2A2 / SERCA2
U49393 M. musculus IIA 141 Ca2+ ATP2A3 / SERCA3
P04192 O. cuniculus IIA 141 Ca2+ ATP2A2 / SERCA2
P20647 O. cuniculus IIA 141 Ca2+ ATP2A2 / SERCA2
P11508 R. norvegicus IIA 141 Ca2+ ATP2A2 / SERCA2
P11507 R. norvegicus IIA 141 Ca2+ ATP2A2 / SERCA2
P11606 Sus scrofa IIA 141 Ca2+ ATP2A2 / SERCA2
P11607 S. scrofa IIA 141 Ca2+ ATP2A2 / SERCA2
Q00804 O. cuniculus IIB 124 Ca2+ ATP2B1 / PMCA1
P11505 R. norvegicus IIB 124 Ca2+ ATP2B1 / PMCA1
P23220 S. scrofa IIB 124 Ca2+ ATP2B1 / PMCA1
J05087 R. norvegicus IIB 125 Ca2+ ATP2B3 / PMCA3
P11506 R. norvegicus IIB 126 Ca2+ ATP2B2 / PMCA2
P30714 Bufo marinus IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P50997 Canis familiaris IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P18907 Equus caballus IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P09572 G. gallus IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P04074 Ovis aries IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P06685 R. norvegicus IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P05024 S. scrofa IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P18874 S. scrofa IIC 104 Na+/K+ ATP1A3 / NaKalpha3
U10108 Xenopus laevis IIC 104 Na+/K+ ATP1A1 / NaKalpha1
P24798 G. gallus IIC 106 Na+/K+ ATP1A3 / NaKalpha3
P06687 R. norvegicus IIC 106 Na+/K+ ATP1A3 / NaKalpha3
P24797 G. gallus IIC 109 Na+/K+ ATP1A2 / NaKalpha2
P06686 R. norvegicus IIC 109 Na+/K+ ATP1A2 / NaKalpha2
P50996 C. familiaris IIC 112 H+/K+ ATP4A
U17282 M. musculus IIC 112 H+/K+
P27112 O. cuniculus IIC 112 H+/K+ ATP4A
P09626 R. norvegicus IIC 112 H+/K+ ATP4A
P19156 S. scrofa IIC 112 H+/K+ ATP4A
Q01896 Saccharomyces cerevisiae IID 94
ENA2 / ydr039c
Z74334 S. cerevisiae IID 94
ENA5 / ydr038c
U72148 Lycopersicon esculentum IIIA 67
LHA4
P20649 Arabidopsis thaliana IIIA 68 H+ AHA1
P22180 L. esculentum IIIA 78
LHA1
Q08435 Nicotiana plumbaginifolia IIIA 78
PMA1
Q08436 N. plumbaginifolia IIIA 78
PMA3
X76536 Solanum tuberosum IIIA 78
PHA1
P11718 Leishmania donovani IIIA 81
ATPase1a
U75321 M. musculus IV 14 PL

Footnotes:
a The accession numbers starting with a Q or P are from the SWISS-PROT database. All other accession numbers are from the EMBL database
b The sequence numbers refer to the numbers defined in Table 1
c The ion specificity of the P-type ATPases is shown, when it has been experimentally shown



Table 3.
Distribution of cloned P-type ATPases according to phylogenetic relationship a


ATPase type

Organism
Total		 IA
K		 IB
HM		 IIA
Ca		 IIB
Ca		 IIC
Na/K		 IIC
H/K		 IID
Na		 IIIA
H		 IIIB
Mg		 IV
PL		 V
NAS		 Othersb
Bacteria
Escherichia coli 4 1 2 0 0 0 0 0 0 1 0 0 0
Haemophilus influenzae 1 0 1 0 0 0 0 0 0 0 0 0 0
Mycobacterium tuberculosis 10 1 5 1 - - - - - - - - 3
Mycoplasma genitalium 1 0 0 0 0 0 0 0 0 0 0 0 1
Mycoplasma pneumoniae 1 0 0 0 0 0 0 0 0 0 0 0 1
Synechocystis PCC6803 9 1 4 3 0 0 0 0 0 0 0 0 1
Archaea
Methanococcus jannaschii 1 0 0 0 0 0 0 0 1 0 0 0 0
Eukarya
protozoa
Plasmodium falciparum 4 - - 2 - - - - - - 1 1 -
fungi
Saccharomyces cerevisiae 16 0 2 1 1 0 0 3(2) 2 0 5 2 0
Schizosaccharomyces pombe 5 - - - - - - 1 2 - 2 - -
plants
Arabidopsis thaliana 8 - - 1 1 - - - 6(2) - - - -
animals
Caenorhabditis elegans 8 - - - 1 2 - - - - 3 2 -
Rattus norvegicus 14c - 2 3(2c) 4 3 2 - - - - - -
Homo sapiens 17c - 2 5(2c) 4(3) 4(3) 2(1) - - - - - -

Footnotes:
a The categories in the table correspond to the branches found in the phylogenetic tree in Fig. 6. The figures in parentheses give the number of closely related ATPases from the groups which are not included in the phylogenetic analysis. Abbreviations: HM: heavy metals; PL: phospholipids; NAS: no assigned specificity
b This group contains bacterial ATPases, for which the ion specificity is not known and which do not group into any of the major branches indicated in Fig. 6
c Two of the proteins in each of these groups originate from one gene by different splicing




Table 4.
Expressed sequence tags in three eukaryotic organisms with similarity to P-type ATPases a

Arabidopsis thaliana
IB
HM
3-6 b 		IIA
Ca
3 		IIB
Ca
4-8 		IIC
Na/K+H/K
- 		III
H
5-6 		IV
PL
2-3 		V
NAS
1
N96835
T43098
T43560
T46552
W43689
Z33730
 R64945
Z37285
Seq. 152
[2 ;-]
 H37540
N65090
N96705
R65015
(T46834) c
R84090
(T43417)
T41649
(T41650)
Z25618
Seq .120 d
[2;-] e
F13883
N38709
N96803
P20649
[24;3]
Seq. 68
[32;10]
Seq. 69
[2;0]
Seq. 74
[0;-]
Seq. 80
[0;-]
 N96084
T45045
T88130
 R65211
(R65219)
Caenorhabditis elegans
IB
HM
1 		IIA
Ca
3-4 		IIB
Ca
1 		IIC
Na/K+H/K
5-7 		III
H
- 		IV
PL
5 		V
NAS
4-5
D36097
(D37525;
D67367)
 C11879
C13112
(C13651;
C13948;
D34934;
D68093;
D68790;
D70495;
D74177;
D74205;
D75938)
C13654
D67762
(M89247)
 Seq. 127
[13;0]
 D27090
D27840
(D64489)
D32312
(D64530)
D35686
(D68187)
D72536
(Z14852)
Seq. 98
[4;0]
Seq. 101
[13;-]
D27733
(D67512)
D34761
(C12815;
D34857;
D36536;
D68551)
D35311
(D36265;
D36990;
D37399)
Seq. 8
[4;0]
Seq. 11
[16;0]
 C12075
(D37337)
D35844
D69289
Seq. 2
[6;0]
Seq. 3
[0;0]
Seq. 5
[7;0]
Homo sapiens
IB
HM
3 		IIA
Ca
5-10 		IIB
Ca
4 		IIC
Na/K+H/K
5-8 		III
H
- 		IV
PL
3-6 		V
NAS
2-4
Z16260
Seq. 49
[4;1]
Seq. 51
[2;-]
 F00478
F00875
F01249
(F18895)
H14052
H82605
N31343
(N56068)
N40047
Seq. 141 f
[58;24]
P16614 f
[3;0]
Z69881
[5;0]
 Seq. 123
[6;-]
Seq. 124
[25;9]
Seq. 125
[0;-]
Seq. 126
[6;1]
 R88986
T19577
W22378
W22714
Seq. 104
[51;12]
Seq. 106
[21;0]
Seq. 109
[32;13]
Seq. 112
[4;0]
Seq. 115
[0;-]
D44622
H13657
(R17452;
R50093;
R20441)
H26328
H30693
(R51412;
R87856)
H97619
(R81633;
T81806)
W26763
 T19151
H16899
(R12888;
R48894;
R86015)
R50051
T72002


Footnotes:
a The expressed sequence tags (ESTs) are placed in the groups of ATPases to which they show the highest similarity on amino acid basis
b The figures give an estimate of how many independent genes the ESTs are representing. The lower figure is based on the differences in similarity among the ESTs to the known P-type ATPases and the higher figure is the maximal possible number of independent genes with the available ESTs.
c EST clones placed in parenthesis depict EST clones overlapping with the EST clone placed in the above position. Abbreviations are as in Table 3
d The accession number or sequence number show an already cloned P-type ATPase. The sequence numbers are as in Table 1. Database accession numbers are given for sequences not included in the phylogenetic analysis
e The figures in square brackets are the total number of ESTs aligning to the mRNA and the ESTs aligning to the 3' untranslated region of the mRNA respectively. A dash indicates that the 3' untranslated region was not available
f Seq. 141 and P16614 are both derived from the same gene as two different splicing products. The ESTs which are identical to both sequences are shown under seq. 141