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3M2V
Asym. Unit
Info
Asym.Unit (452 KB)
Biol.Unit 1 (442 KB)
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(1)
Title
:
STRUCTURAL INSIGHT INTO METHYL-COENZYME M REDUCTASE CHEMISTRY USING COENZYME B ANALOGUES
Authors
:
P. E. Cedervall, M. Dey, S. W. Ragsdale, C. M. Wilmot
Date
:
08 Mar 10 (Deposition) - 15 Sep 10 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Methyl-Coenzyme M Reductase, Nickel, Metal-Binding, Methanogenesis, Methylation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. E. Cedervall, M. Dey, A. R. Pearson, S. W. Ragsdale, C. M. Wilmot
Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues.
Biochemistry V. 49 7683 2010
[
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Hetero Components
(13, 29)
Info
All Hetero Components
01a: ACETATE ION (ACTa)
02a: 5-METHYL-ARGININE (AGMa)
02b: 5-METHYL-ARGININE (AGMb)
03a: 1-THIOETHANESULFONIC ACID (COMa)
03b: 1-THIOETHANESULFONIC ACID (COMb)
04a: 1,2-ETHANEDIOL (EDOa)
04b: 1,2-ETHANEDIOL (EDOb)
04c: 1,2-ETHANEDIOL (EDOc)
04d: 1,2-ETHANEDIOL (EDOd)
05a: FACTOR 430 (F43a)
05b: FACTOR 430 (F43b)
06a: THIOGLYCIN (GL3a)
06b: THIOGLYCIN (GL3b)
08a: 2-METHYL-GLUTAMINE (MGNa)
08b: 2-METHYL-GLUTAMINE (MGNb)
07a: MAGNESIUM ION (MGa)
07b: MAGNESIUM ION (MGb)
07c: MAGNESIUM ION (MGc)
07d: MAGNESIUM ION (MGd)
07e: MAGNESIUM ION (MGe)
09a: N1-METHYLATED HISTIDINE (MHSa)
09b: N1-METHYLATED HISTIDINE (MHSb)
10a: S-METHYLCYSTEINE (SMCa)
10b: S-METHYLCYSTEINE (SMCb)
11a: COENZYME B (TP7a)
11b: COENZYME B (TP7b)
12a: O-PHOSPHONO-N-(8-SULFANYLOCTANOYL)... (XP8a)
12b: O-PHOSPHONO-N-(8-SULFANYLOCTANOYL)... (XP8b)
13a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
3
COM
2
Ligand/Ion
1-THIOETHANESULFONIC ACID
4
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
5
F43
2
Ligand/Ion
FACTOR 430
6
GL3
2
Mod. Amino Acid
THIOGLYCIN
7
MG
5
Ligand/Ion
MAGNESIUM ION
8
MGN
2
Mod. Amino Acid
2-METHYL-GLUTAMINE
9
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
10
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
11
TP7
2
Ligand/Ion
COENZYME B
12
XP8
2
Ligand/Ion
O-PHOSPHONO-N-(8-SULFANYLOCTANOYL)-L-THREONINE
13
ZN
1
Ligand/Ion
ZINC ION
[
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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
ACT A:555 , HOH A:706 , HOH A:1599 , HOH A:2285 , HOH A:3828 , HOH A:3971
BINDING SITE FOR RESIDUE MG A 551
02
AC2
SOFTWARE
ALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:647 , HOH A:666 , HOH A:668 , HOH A:671 , HOH A:690 , HOH A:692 , HOH A:788 , GLY D:326 , GLY D:327 , VAL D:328 , GLY D:329 , PHE D:330 , THR D:331 , GLN D:332 , TYR D:333 , PHE D:396 , GLY D:397 , GLY D:442 , PHE D:443 , COM D:552 , SER E:365 , ILE E:366 , TYR E:367 , LEU F:117 , SER F:118 , GLY F:119 , LYS F:153 , SER F:154 , VAL F:155 , HIS F:156 , HIS F:158 , HOH F:582
BINDING SITE FOR RESIDUE F43 A 1
03
AC3
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , PHE A:330 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:588 , HOH A:600 , HOH A:678 , HOH A:3684 , PHE B:362 , TYR B:367 , GLY B:369 , HIS B:379 , ILE B:380 , HOH B:479 , ARG D:225 , LYS D:256 , MHS D:257
BINDING SITE FOR RESIDUE TP7 A 552
04
AC4
SOFTWARE
TYR A:333 , PHE A:443 , TYR A:444 , HOH A:3682 , PHE B:361 , SER B:365 , TYR B:367 , LEU C:117 , ARG C:120 , F43 D:551
BINDING SITE FOR RESIDUE COM A 553
05
AC5
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , PHE A:330 , PHE A:443 , MET A:480 , HOH A:588 , HOH A:600 , HOH A:678 , HOH A:3684 , PHE B:361 , PHE B:362 , TYR B:367 , GLY B:369 , HIS B:379 , ILE B:380 , HOH B:479 , ARG D:225 , LYS D:256 , MHS D:257
BINDING SITE FOR RESIDUE XP8 A 554
06
AC6
SOFTWARE
VAL A:519 , LYS A:531 , PHE A:537 , GLU A:538 , MG A:551 , HOH A:1396 , HOH A:2285 , HOH A:3828 , HOH A:3988 , HOH A:4121
BINDING SITE FOR RESIDUE ACT A 555
07
AC7
SOFTWARE
ASP A:516 , LEU A:518 , PHE A:520 , ASP A:521 , HOH A:1599 , HOH A:2603
BINDING SITE FOR RESIDUE EDO A 556
08
AC8
SOFTWARE
TYR A:348 , HOH A:4125
BINDING SITE FOR RESIDUE EDO A 557
09
AC9
SOFTWARE
HOH B:1305 , HOH B:3547 , HOH B:3548 , HOH B:3549 , HOH B:3550
BINDING SITE FOR RESIDUE MG B 1
10
BC1
SOFTWARE
ASP B:271 , HOH B:811 , HOH B:1206 , HOH B:3076 , HOH B:4122
BINDING SITE FOR RESIDUE MG B 444
11
BC2
SOFTWARE
GLU C:30 , HOH C:1095 , HOH C:3555 , HOH C:3556 , HOH C:3557 , HOH C:3558
BINDING SITE FOR RESIDUE MG C 250
12
BC3
SOFTWARE
GLY A:326 , GLY A:327 , VAL A:328 , GLY A:329 , PHE A:330 , THR A:331 , GLN A:332 , TYR A:333 , PHE A:396 , GLY A:397 , GLY A:442 , PHE A:443 , COM A:553 , SER B:365 , ILE B:366 , TYR B:367 , LEU C:117 , SER C:118 , GLY C:119 , LYS C:153 , SER C:154 , VAL C:155 , HIS C:156 , HIS C:158 , HOH C:526 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243 , HOH D:567 , HOH D:594 , HOH D:641 , HOH D:665 , HOH D:707 , HOH D:716
BINDING SITE FOR RESIDUE F43 D 551
13
BC4
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , SER D:325 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:566 , HOH D:571 , HOH D:579 , HOH D:627 , HOH D:660 , PHE E:362 , TYR E:367 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE TP7 D 1
14
BC5
SOFTWARE
F43 A:1 , TYR D:333 , PHE D:443 , TYR D:444 , PHE E:361 , SER E:365 , TYR E:367 , LEU F:117 , ARG F:120 , HOH F:760
BINDING SITE FOR RESIDUE COM D 552
15
BC6
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , PHE D:330 , PHE D:443 , MET D:480 , HOH D:566 , HOH D:571 , HOH D:579 , HOH D:627 , HOH D:660 , PHE E:362 , TYR E:367 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE XP8 D 553
16
BC7
SOFTWARE
LYS D:22 , GLU F:164 , GLY F:166
BINDING SITE FOR RESIDUE EDO D 554
17
BC8
SOFTWARE
TYR D:348
BINDING SITE FOR RESIDUE EDO D 555
18
BC9
SOFTWARE
ARG A:102 , SER A:215 , ARG A:216 , CYS A:218 , ARG D:102 , SER D:215 , ARG D:216 , CYS D:218
BINDING SITE FOR RESIDUE ZN D 556
19
CC1
SOFTWARE
GLU F:30 , HOH F:1294 , HOH F:3551 , HOH F:3552 , HOH F:3553 , HOH F:3554
BINDING SITE FOR RESIDUE MG F 250
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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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
(5, 10)
Info
All SCOP Domains
1a: SCOP_d3m2va2 (A:270-549)
1b: SCOP_d3m2vd2 (D:270-549)
2a: SCOP_d3m2vb2 (B:189-443)
2b: SCOP_d3m2ve2 (E:189-443)
3a: SCOP_d3m2va1 (A:2-269)
3b: SCOP_d3m2vd1 (D:2-269)
4a: SCOP_d3m2vb1 (B:2-188)
4b: SCOP_d3m2ve1 (E:2-188)
5a: SCOP_d3m2vc_ (C:)
5b: SCOP_d3m2vf_ (F:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Superfamily
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Family
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(26)
Protein domain
:
Alpha chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
1a
d3m2va2
A:270-549
1b
d3m2vd2
D:270-549
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
2a
d3m2vb2
B:189-443
2b
d3m2ve2
E:189-443
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Methyl-coenzyme M reductase subunits
(42)
Family
:
Methyl-coenzyme M reductase alpha and beta chain N-terminal domain
(26)
Protein domain
:
Alpha chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
3a
d3m2va1
A:2-269
3b
d3m2vd1
D:2-269
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
4a
d3m2vb1
B:2-188
4b
d3m2ve1
E:2-188
Family
:
Methyl-coenzyme M reductase gamma chain
(14)
Protein domain
:
Methyl-coenzyme M reductase gamma chain
(14)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(12)
5a
d3m2vc_
C:
5b
d3m2vf_
F:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_MCR_alpha_3m2vD01 (D:316-441)
1b: PFAM_MCR_alpha_3m2vD02 (D:316-441)
2a: PFAM_MCR_alpha_N_3m2vD03 (D:2-268)
2b: PFAM_MCR_alpha_N_3m2vD04 (D:2-268)
3a: PFAM_MCR_beta_3m2vE01 (E:189-442)
3b: PFAM_MCR_beta_3m2vE02 (E:189-442)
4a: PFAM_MCR_beta_N_3m2vE03 (E:6-187)
4b: PFAM_MCR_beta_N_3m2vE04 (E:6-187)
5a: PFAM_MCR_gamma_3m2vF01 (F:2-248)
5b: PFAM_MCR_gamma_3m2vF02 (F:2-248)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: MCR_alpha]
(8)
Family
:
MCR_alpha
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
1a
MCR_alpha-3m2vD01
D:316-441
1b
MCR_alpha-3m2vD02
D:316-441
Clan
:
no clan defined [family: MCR_alpha_N]
(8)
Family
:
MCR_alpha_N
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
2a
MCR_alpha_N-3m2vD03
D:2-268
2b
MCR_alpha_N-3m2vD04
D:2-268
Clan
:
no clan defined [family: MCR_beta]
(8)
Family
:
MCR_beta
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
3a
MCR_beta-3m2vE01
E:189-442
3b
MCR_beta-3m2vE02
E:189-442
Clan
:
no clan defined [family: MCR_beta_N]
(8)
Family
:
MCR_beta_N
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
4a
MCR_beta_N-3m2vE03
E:6-187
4b
MCR_beta_N-3m2vE04
E:6-187
Clan
:
no clan defined [family: MCR_gamma]
(8)
Family
:
MCR_gamma
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
5a
MCR_gamma-3m2vF01
F:2-248
5b
MCR_gamma-3m2vF02
F:2-248
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