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1MFZ
Asym. Unit
Info
Asym.Unit (276 KB)
Biol.Unit 1 (137 KB)
Biol.Unit 2 (135 KB)
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(1)
Title
:
PARTIALLY REFINED 2.8 A CRYSTAL STRUCTURE OF GDP-MANNOSE DEHYDROGENASE FROM P. AERUGINOSA
Authors
:
C. F. Snook, P. A. Tipton, L. J. Beamer
Date
:
14 Aug 02 (Deposition) - 06 May 03 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Rossmann Fold, Domain-Swapped Dimer, Enzyme Complex With Cofactor And Product, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
C. F. Snook, P. A. Tipton, L. J. Beamer
The Crystal Structure Of Gdp-Mannose Dehydrogenase: A Key Enzyme In Alginate Biosynthesis Of P. Aeruginosa
Biochemistry V. 42 4658 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 40)
Info
All Hetero Components
1a: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXa)
1b: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXb)
1c: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXc)
1d: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GDX
4
Ligand/Ion
GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
2
MSE
36
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU C:157 , PHE C:158 , LEU C:159 , ARG C:160 , GLU C:161 , LYS C:210 , ASN C:214 , HIS C:217 , VAL C:221 , ASN C:225 , TYR D:256 , TYR D:257 , MSE D:258 , ARG D:259 , PHE D:262 , PHE D:264 , GLY D:265 , CYS D:268 , LEU D:269 , PHE D:323 , LYS D:324 , HOH D:510
BINDING SITE FOR RESIDUE GDX D 501
2
AC2
SOFTWARE
TYR C:256 , TYR C:257 , MSE C:258 , ARG C:259 , GLY C:261 , PHE C:262 , PHE C:264 , GLY C:265 , CYS C:268 , PHE C:323 , LYS C:324 , TYR D:10 , GLU D:157 , PHE D:158 , LEU D:159 , ARG D:160 , GLU D:161 , LYS D:210 , ASN D:214 , HIS D:217 , VAL D:221 , ASN D:225 , HOH D:519
BINDING SITE FOR RESIDUE GDX D 502
3
AC3
SOFTWARE
GLU A:157 , PHE A:158 , LEU A:159 , ARG A:160 , GLU A:161 , LYS A:210 , ASN A:214 , HIS A:217 , VAL A:221 , ASN A:225 , LEU B:251 , TYR B:256 , TYR B:257 , MSE B:258 , ARG B:259 , PHE B:262 , PHE B:264 , GLY B:265 , CYS B:268 , LEU B:269 , PHE B:323 , LYS B:324 , HOH B:506 , HOH B:507
BINDING SITE FOR RESIDUE GDX B 503
4
AC4
SOFTWARE
TYR A:256 , TYR A:257 , MSE A:258 , ARG A:259 , GLY A:261 , PHE A:262 , PHE A:264 , GLY A:265 , CYS A:268 , LEU A:269 , PHE A:323 , LYS A:324 , GLU B:157 , PHE B:158 , LEU B:159 , ARG B:160 , GLU B:161 , LYS B:210 , ASN B:214 , HIS B:217 , VAL B:221 , ASN B:225
BINDING SITE FOR RESIDUE GDX B 504
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1mfza1 (A:203-300)
1b: SCOP_d1mfzc1 (C:203-300)
1c: SCOP_d1mfzd1 (D:203-300)
1d: SCOP_d1mfzb1 (B:203-300)
2a: SCOP_d1mfza3 (A:301-436)
2b: SCOP_d1mfzc3 (C:301-436)
2c: SCOP_d1mfzd3 (D:301-436)
2d: SCOP_d1mfzb3 (B:301-436)
3a: SCOP_d1mfza2 (A:1-202)
3b: SCOP_d1mfzc2 (C:1-202)
3c: SCOP_d1mfzd2 (D:1-202)
3d: SCOP_d1mfzb2 (B:1-202)
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)
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain
(5)
Protein domain
:
GDP-mannose 6-dehydrogenase, middle domain
(3)
Pseudomonas aeruginosa [TaxId: 287]
(3)
1a
d1mfza1
A:203-300
1b
d1mfzc1
C:203-300
1c
d1mfzd1
D:203-300
1d
d1mfzb1
B:203-300
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
(5)
Family
:
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
(5)
Protein domain
:
GDP-mannose 6-dehydrogenase, GDP-binding domain
(3)
Pseudomonas aeruginosa [TaxId: 287]
(3)
2a
d1mfza3
A:301-436
2b
d1mfzc3
C:301-436
2c
d1mfzd3
D:301-436
2d
d1mfzb3
B:301-436
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
6-phosphogluconate dehydrogenase-like, N-terminal domain
(69)
Protein domain
:
GDP-mannose 6-dehydrogenase
(3)
Pseudomonas aeruginosa [TaxId: 287]
(3)
3a
d1mfza2
A:1-202
3b
d1mfzc2
C:1-202
3c
d1mfzd2
D:1-202
3d
d1mfzb2
B:1-202
[
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]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1mfzA01 (A:2-202)
1b: CATH_1mfzC01 (C:2-202)
1c: CATH_1mfzD01 (D:2-202)
1d: CATH_1mfzA03 (A:235-436)
1e: CATH_1mfzB03 (B:235-436)
1f: CATH_1mfzC03 (C:235-436)
1g: CATH_1mfzD03 (D:235-436)
1h: CATH_1mfzB01 (B:2-202)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pseudomonas aeruginosa. Organism_taxid: 287.
(5)
1a
1mfzA01
A:2-202
1b
1mfzC01
C:2-202
1c
1mfzD01
D:2-202
1d
1mfzA03
A:235-436
1e
1mfzB03
B:235-436
1f
1mfzC03
C:235-436
1g
1mfzD03
D:235-436
1h
1mfzB01
B:2-202
[
close CATH info
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_UDPG_MGDP_dh_1mfzD01 (D:203-300)
1b: PFAM_UDPG_MGDP_dh_1mfzD02 (D:203-300)
1c: PFAM_UDPG_MGDP_dh_1mfzD03 (D:203-300)
1d: PFAM_UDPG_MGDP_dh_1mfzD04 (D:203-300)
2a: PFAM_UDPG_MGDP_dh_N_1mfzD05 (D:1-190)
2b: PFAM_UDPG_MGDP_dh_N_1mfzD06 (D:1-190)
2c: PFAM_UDPG_MGDP_dh_N_1mfzD07 (D:1-190)
2d: PFAM_UDPG_MGDP_dh_N_1mfzD08 (D:1-190)
3a: PFAM_UDPG_MGDP_dh_C_1mfzD09 (D:317-423)
3b: PFAM_UDPG_MGDP_dh_C_1mfzD10 (D:317-423)
3c: PFAM_UDPG_MGDP_dh_C_1mfzD11 (D:317-423)
3d: PFAM_UDPG_MGDP_dh_C_1mfzD12 (D:317-423)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
UDPG_MGDP_dh
(10)
Pseudomonas aeruginosa
(3)
1a
UDPG_MGDP_dh-1mfzD01
D:203-300
1b
UDPG_MGDP_dh-1mfzD02
D:203-300
1c
UDPG_MGDP_dh-1mfzD03
D:203-300
1d
UDPG_MGDP_dh-1mfzD04
D:203-300
Clan
:
NADP_Rossmann
(1239)
Family
:
UDPG_MGDP_dh_N
(10)
Pseudomonas aeruginosa
(3)
2a
UDPG_MGDP_dh_N-1mfzD05
D:1-190
2b
UDPG_MGDP_dh_N-1mfzD06
D:1-190
2c
UDPG_MGDP_dh_N-1mfzD07
D:1-190
2d
UDPG_MGDP_dh_N-1mfzD08
D:1-190
Clan
:
no clan defined [family: UDPG_MGDP_dh_C]
(10)
Family
:
UDPG_MGDP_dh_C
(10)
Pseudomonas aeruginosa
(3)
3a
UDPG_MGDP_dh_C-1mfzD09
D:317-423
3b
UDPG_MGDP_dh_C-1mfzD10
D:317-423
3c
UDPG_MGDP_dh_C-1mfzD11
D:317-423
3d
UDPG_MGDP_dh_C-1mfzD12
D:317-423
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