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3H65
Asym. Unit
Info
Asym.Unit (65 KB)
Biol.Unit 1 (115 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF C176A MUTATED [FE]-HYDROGENASE (HMD) HOLOENZYME IN COMPLEX WITH METHYLENETETRAHYDROMETHANOPTERIN
Authors
:
T. Hiromoto, E. Warkentin, S. Shima, U. Ermler
Date
:
23 Apr 09 (Deposition) - 01 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Rossmann Fold, Helix Bundle, Complex With Iron Guanylyl Pyridinol Cofactor, C176A Mutant, Complex With Methylenetetrahydromethanopterin, Methanogenesis, One-Carbon Metabolism, Oxidoreductase
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Reference
:
T. Hiromoto, E. Warkentin, J. Moll, U. Ermler, S. Shima
The Crystal Structure Of An [Fe]-Hydrogenase-Substrate Complex Reveals The Framework For H2 Activation.
Angew. Chem. Int. Ed. Engl. V. 48 6457 2009
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: CARBON MONOXIDE (CMOa)
1b: CARBON MONOXIDE (CMOb)
2a: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTVa)
3a: FE (II) ION (FE2a)
4a: 5,10-DIMETHYLENE TETRAHYDROMETHANO... (H4Ma)
5a: 5'-O-[(S)-HYDROXY{[2-HYDROXY-3,5-D... (I2Ca)
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No.
Name
Count
Type
Full Name
1
CMO
2
Ligand/Ion
CARBON MONOXIDE
2
DTV
1
Ligand/Ion
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3
FE2
1
Ligand/Ion
FE (II) ION
4
H4M
1
Ligand/Ion
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
5
I2C
1
Ligand/Ion
5'-O-[(S)-HYDROXY{[2-HYDROXY-3,5-DIMETHYL-6-(2-OXOETHYL)PYRIDIN-4-YL]OXY}PHOSPHORYL]GUANOSINE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
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Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:6 , GLY A:7 , GLY A:9 , CYS A:10 , THR A:13 , HIS A:14 , SER A:63 , ASP A:64 , PRO A:65 , PRO A:114 , PRO A:115 , CYS A:118 , ASP A:135 , TRP A:148 , LEU A:149 , PRO A:150 , ILE A:158 , ALA A:175 , ALA A:176 , THR A:177 , PRO A:202 , FE2 A:360 , CMO A:361 , CMO A:362 , DTV A:363 , HOH A:369 , HOH A:398 , HOH A:415 , HOH A:420
BINDING SITE FOR RESIDUE I2C A 359
2
AC2
SOFTWARE
I2C A:359 , CMO A:361 , CMO A:362 , DTV A:363
BINDING SITE FOR RESIDUE FE2 A 360
3
AC3
SOFTWARE
TRP A:148 , CYS A:204 , VAL A:205 , PRO A:206 , I2C A:359 , FE2 A:360 , CMO A:362 , DTV A:363
BINDING SITE FOR RESIDUE CMO A 361
4
AC4
SOFTWARE
ALA A:176 , CYS A:204 , I2C A:359 , FE2 A:360 , CMO A:361 , DTV A:363
BINDING SITE FOR RESIDUE CMO A 362
5
AC5
SOFTWARE
THR A:13 , ALA A:176 , I2C A:359 , FE2 A:360 , CMO A:361 , CMO A:362
BINDING SITE FOR RESIDUE DTV A 363
6
AC6
SOFTWARE
LYS A:151 , GLY A:152 , CYS A:250 , ASP A:251 , MET A:252 , SER A:254 , LEU A:275 , PRO A:278 , ASP A:280 , PHE A:281 , MET A:284 , THR A:317 , SER A:320 , MET A:321 , HOH A:365 , HOH A:450 , HOH A:460
BINDING SITE FOR RESIDUE H4M A 364
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3h65a2 (A:243-345)
2a: SCOP_d3h65a1 (A:1-242)
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Protein Domains
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Organisms
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(
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Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
HMD dimerization domain-like
(6)
Protein domain
:
5,10-methenyltetrahydromethanopterin hydrogenase, HMD
(6)
Methanocaldococcus jannaschii [TaxId: 2190]
(6)
1a
d3h65a2
A:243-345
Class
:
Alpha and beta proteins (a/b)
(23833)
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
:
5,10-methenyltetrahydromethanopterin hydrogenase, HMD
(6)
Methanocaldococcus jannaschii [TaxId: 2190]
(6)
2a
d3h65a1
A:1-242
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CATH Domains
(0, 0)
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Pfam Domains
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Chain A
Asymmetric Unit 1
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