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2V5H
Asym. Unit
Info
Asym.Unit (376 KB)
Biol.Unit 1 (361 KB)
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(1)
Title
:
CONTROLLING THE STORAGE OF NITROGEN AS ARGININE: THE COMPLEX OF PII AND ACETYLGLUTAMATE KINASE FROM SYNECHOCOCCUS ELONGATUS PCC 7942
Authors
:
J. L. Llacer, C. Marco-Marin, F. Gil-Ortiz, I. Fita, V. Rubio
Date
:
04 Jul 07 (Deposition) - 16 Oct 07 (Release) - 10 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Amino-Acid Biosynthesis, Transcription Regulation, Transferase, Cyanobacteria, Transcription, N-Acetyl-L-Glutamate Kinase, Pii Signal Protein, Nucleotide-Binding, Acetylglutamate, Phosphorylation, Amino Acid Kinase, Glnb, Kinase, Trimer, Hexamer, Atp-Binding, Arginine Inhibition, Arginine Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Llacer, A. Contreras, K. Forchhammer, C. Marco-Marin, F. Gil-Ortiz, R. Maldonado, I. Fita, V. Rubio
The Crystal Structure Of The Complex Of Pii And Acetylglutamate Kinase Reveals How Pii Controls The Storage Of Nitrogen As Arginine.
Proc. Natl. Acad. Sci. Usa V. 104 17644 2007
[
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Hetero Components
(4, 19)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
2a: GLYCEROL (GOLa)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
4a: N-ACETYL-L-GLUTAMATE (NLGa)
4b: N-ACETYL-L-GLUTAMATE (NLGb)
4c: N-ACETYL-L-GLUTAMATE (NLGc)
4d: N-ACETYL-L-GLUTAMATE (NLGd)
4e: N-ACETYL-L-GLUTAMATE (NLGe)
4f: N-ACETYL-L-GLUTAMATE (NLGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
6
Ligand/Ion
CHLORIDE ION
2
GOL
1
Ligand/Ion
GLYCEROL
3
NA
6
Ligand/Ion
SODIUM ION
4
NLG
6
Ligand/Ion
N-ACETYL-L-GLUTAMATE
[
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]
Sites
(19, 19)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:69 , GLY A:70 , GLY A:71 , ILE A:74 , ARG A:92 , SER A:174 , ASN A:185 , ILE A:186 , ASN A:187 , ALA A:188
BINDING SITE FOR RESIDUE NLG A1292
02
AC2
SOFTWARE
GLU A:277 , THR A:280 , HOH A:2027 , HOH A:2028
BINDING SITE FOR RESIDUE NA A1293
03
AC3
SOFTWARE
GLY B:69 , GLY B:70 , GLY B:71 , ILE B:74 , ARG B:92 , SER B:174 , ASN B:185 , ILE B:186 , ALA B:188
BINDING SITE FOR RESIDUE NLG B1297
04
AC4
SOFTWARE
GLU B:277 , THR B:280 , HOH B:2022
BINDING SITE FOR RESIDUE NA B1298
05
AC5
SOFTWARE
GLY C:69 , GLY C:70 , GLY C:71 , ILE C:74 , ARG C:92 , SER C:174 , ASN C:185 , ALA C:188
BINDING SITE FOR RESIDUE NLG C1292
06
AC6
SOFTWARE
GLU C:277 , THR C:280 , HOH C:2014 , HOH C:2015
BINDING SITE FOR RESIDUE NA C1293
07
AC7
SOFTWARE
GLY D:69 , GLY D:70 , GLY D:71 , ILE D:74 , ARG D:92 , ASN D:185 , ALA D:188
BINDING SITE FOR RESIDUE NLG D1294
08
AC8
SOFTWARE
GLU D:277 , THR D:280
BINDING SITE FOR RESIDUE NA D1295
09
AC9
SOFTWARE
GLY E:69 , GLY E:70 , GLY E:71 , ILE E:74 , ARG E:92 , ASN E:185 , ALA E:188
BINDING SITE FOR RESIDUE NLG E1294
10
BC1
SOFTWARE
GLY D:181 , LYS E:112 , ASP E:113 , ARG E:117
BINDING SITE FOR RESIDUE GOL E1295
11
BC2
SOFTWARE
GLU E:277 , THR E:280
BINDING SITE FOR RESIDUE NA E1296
12
BC3
SOFTWARE
GLY F:69 , GLY F:70 , GLY F:71 , ARG F:92 , VAL F:149 , ASN F:185 , ALA F:188
BINDING SITE FOR RESIDUE NLG F1293
13
BC4
SOFTWARE
GLU F:277 , THR F:280 , HOH F:2022 , HOH F:2023
BINDING SITE FOR RESIDUE NA F1294
14
BC5
SOFTWARE
GLN G:39 , GLY G:87 , ASP G:88 , ARG I:103
BINDING SITE FOR RESIDUE CL G1112
15
BC6
SOFTWARE
ARG G:103 , ILE H:86 , GLY H:87 , HOH H:2011
BINDING SITE FOR RESIDUE CL H1109
16
BC7
SOFTWARE
ARG H:101 , ARG H:103 , ILE I:86 , GLY I:87 , ASP I:88 , HOH I:2008
BINDING SITE FOR RESIDUE CL H1110
17
BC8
SOFTWARE
ARG J:103 , ILE K:86 , GLY K:87
BINDING SITE FOR RESIDUE CL J1111
18
BC9
SOFTWARE
ILE J:86 , GLY J:87 , ARG L:103
BINDING SITE FOR RESIDUE CL J1112
19
CC1
SOFTWARE
ARG K:101 , ARG K:103 , GLY L:87 , ASP L:88 , HOH L:2010
BINDING SITE FOR RESIDUE CL K1109
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(3, 18)
Info
All PROSITE Patterns/Profiles
1: PII_GLNB_DOM (G:1-111,H:1-108,I:1-111,J:1-110,K:...)
2: PII_GLNB_UMP (G:46-51,H:46-51,I:46-51,J:46-51,K:...)
3: PII_GLNB_CTER (G:83-96,H:83-96,I:83-96,J:83-96,K:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PII_GLNB_DOM
PS51343
P-II protein family profile.
GLNB_SYNE7
1-112
6
G:1-111
H:1-108
I:1-111
J:1-110
K:1-108
L:1-109
2
PII_GLNB_UMP
PS00496
P-II protein uridylation site.
GLNB_SYNE7
46-51
6
G:46-51
H:46-51
I:46-51
J:46-51
K:46-51
L:46-51
3
PII_GLNB_CTER
PS00638
P-II protein C-terminal region signature.
GLNB_SYNE7
83-96
6
G:83-96
H:83-96
I:83-96
J:83-96
K:83-96
L:83-96
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2v5hg_ (G:)
1b: SCOP_d2v5hj_ (J:)
1c: SCOP_d2v5hk_ (K:)
1d: SCOP_d2v5hl_ (L:)
1e: SCOP_d2v5hh_ (H:)
1f: SCOP_d2v5hi_ (I:)
2a: SCOP_d2v5ha_ (A:)
2b: SCOP_d2v5hb_ (B:)
2c: SCOP_d2v5hc_ (C:)
2d: SCOP_d2v5hd_ (D:)
2e: SCOP_d2v5he_ (E:)
2f: SCOP_d2v5hf_ (F:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
GlnB-like
(79)
Family
:
Prokaryotic signal transducing protein
(31)
Protein domain
:
PII (product of glnB)
(17)
Cyanobacteria (Synechococcus sp.) pcc 7942 [TaxId: 1131]
(4)
1a
d2v5hg_
G:
1b
d2v5hj_
J:
1c
d2v5hk_
K:
1d
d2v5hl_
L:
1e
d2v5hh_
H:
1f
d2v5hi_
I:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Carbamate kinase-like
(63)
Superfamily
:
Carbamate kinase-like
(63)
Family
:
automated matches
(24)
Protein domain
:
automated matches
(24)
Synechococcus elongatus [TaxId: 1140]
(1)
2a
d2v5ha_
A:
2b
d2v5hb_
B:
2c
d2v5hc_
C:
2d
d2v5hd_
D:
2e
d2v5he_
E:
2f
d2v5hf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2v5hH00 (H:1-108)
1b: CATH_2v5hK00 (K:1-108)
1c: CATH_2v5hI00 (I:1-111)
1d: CATH_2v5hL00 (L:1-109)
1e: CATH_2v5hJ00 (J:1-110)
1f: CATH_2v5hG00 (G:1-111)
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.120, no name defined]
(37)
Synechococcus elongatus. Organism_taxid: 1140. Strain: pcc 7942.
(4)
1a
2v5hH00
H:1-108
1b
2v5hK00
K:1-108
1c
2v5hI00
I:1-111
1d
2v5hL00
L:1-109
1e
2v5hJ00
J:1-110
1f
2v5hG00
G:1-111
[
close CATH info
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_P_II_2v5hL01 (L:4-105)
1b: PFAM_P_II_2v5hL02 (L:4-105)
1c: PFAM_P_II_2v5hL03 (L:4-105)
1d: PFAM_P_II_2v5hL04 (L:4-105)
1e: PFAM_P_II_2v5hL05 (L:4-105)
1f: PFAM_P_II_2v5hL06 (L:4-105)
2a: PFAM_AA_kinase_2v5hF01 (F:30-267)
2b: PFAM_AA_kinase_2v5hF02 (F:30-267)
2c: PFAM_AA_kinase_2v5hF03 (F:30-267)
2d: PFAM_AA_kinase_2v5hF04 (F:30-267)
2e: PFAM_AA_kinase_2v5hF05 (F:30-267)
2f: PFAM_AA_kinase_2v5hF06 (F:30-267)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GlnB-like
(50)
Family
:
P-II
(26)
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
(7)
1a
P-II-2v5hL01
L:4-105
1b
P-II-2v5hL02
L:4-105
1c
P-II-2v5hL03
L:4-105
1d
P-II-2v5hL04
L:4-105
1e
P-II-2v5hL05
L:4-105
1f
P-II-2v5hL06
L:4-105
Clan
:
no clan defined [family: AA_kinase]
(20)
Family
:
AA_kinase
(20)
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
(2)
2a
AA_kinase-2v5hF01
F:30-267
2b
AA_kinase-2v5hF02
F:30-267
2c
AA_kinase-2v5hF03
F:30-267
2d
AA_kinase-2v5hF04
F:30-267
2e
AA_kinase-2v5hF05
F:30-267
2f
AA_kinase-2v5hF06
F:30-267
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