P11558 (MCRA_METTM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Methyl-coenzyme M reductase I subunit alpha
Short name=MCR I alpha
EC=2.8.4.1

Alternative name(s):
Coenzyme-B sulfoethylthiotransferase alpha

Gene names

Name:	mcrA
Ordered Locus Names:	MTBMA_c15480

Organism

Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) [Complete proteome] [HAMAP]

Taxonomic identifier

79929 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanothermobacter

Protein attributes

Sequence length	550 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and an heterodisulfide.
Catalytic activity	Methyl-CoM + CoB = CoM-S-S-CoB + methane.
Cofactor	Binds 2 coenzyme F430 noncovalently per hexamer. Coenzyme F430 is a yellow nickel porphinoid.
Pathway	One-carbon metabolism; methyl-coenzyme M reduction; methane from methyl-coenzyme M: step 1/1.
Subunit structure	Hexamer of two alpha, two beta, and two gamma chains.
Developmental stage	There are two MCR complexes in this bacteria. MCR II is expressed in the early growth phase. Late growth cells contains mostly MCR I.

Ontologies

Keywords
Biological process	Methanogenesis
Ligand	Metal-binding Nickel
Molecular function	Transferase
PTM	Methylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	methanogenesis Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	coenzyme-B sulfoethylthiotransferase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 550

549

Methyl-coenzyme M reductase I subunit alpha

PRO_0000147456

Sites

Metal binding

147

1

Nickel

Amino acid modifications

Modified residue

257

1

Pros-methylhistidine

Modified residue

271

1

5-methylarginine

Modified residue

400

1

2-methylglutamine

Modified residue

445

1

1-thioglycine

Modified residue

452

1

S-methylcysteine

Secondary structure

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550

Helix Strand Turn

Details...

Helix

7 – 13

7

Helix

30 – 33

4

Helix

35 – 51

17

Beta strand

60 – 62

3

Beta strand

71 – 74

4

Beta strand

80 – 82

3

Helix

83 – 86

4

Helix

88 – 90

3

Helix

92 – 102

11

Beta strand

104 – 109

6

Helix

110 – 118

9

Helix

126 – 139

14

Turn

140 – 142

3

Helix

155 – 158

4

Beta strand

162 – 168

7

Helix

170 – 175

6

Helix

178 – 180

3

Helix

184 – 187

4

Helix

190 – 200

11

Beta strand

204 – 209

6

Helix

212 – 217

6

Helix

222 – 239

18

Helix

246 – 256

11

Turn

257 – 259

3

Helix

269 – 271

3

Beta strand

275 – 277

3

Helix

278 – 280

3

Helix

283 – 289

7

Helix

292 – 295

4

Helix

300 – 316

17

Helix

317 – 323

7

Helix

331 – 335

5

Turn

336 – 338

3

Helix

342 – 357

16

Helix

367 – 387

21

Helix

389 – 394

6

Helix

398 – 417

20

Helix

420 – 438

19

Helix

448 – 457

10

Turn

462 – 464

3

Helix

468 – 470

3

Helix

476 – 478

3

Beta strand

482 – 484

3

Helix

485 – 499

15

Helix

507 – 512

6

Beta strand

518 – 520

3

Helix

525 – 533

9

Helix

544 – 546

3

Sequences

	Sequence		Length	Mass (Da)
	P11558 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: D55A724B6CA9EFEE	FASTA	550	60,511
	10 20 30 40 50 60 MADKLFINAL KKKFEESPEE KKTTFYTLGG WKQSERKTEF VNAGKEVAAK RGIPQYNPDI 70 80 90 100 110 120 GTPLGQRVLM PYQVSTTDTY VEGDDLHFVN NAAMQQMWDD IRRTVIVGLN HAHAVIEKRL 130 140 150 160 170 180 GKEVTPETIT HYLETVNHAM PGAAVVQEHM VETHPALVAD SYVKVFTGND EIADEIDPAF 190 200 210 220 230 240 VIDINKQFPE DQAETLKAEV GDGIWQVVRI PTIVSRTCDG ATTSRWSAMQ IGMSMISAYK 250 260 270 280 290 300 QAAGEAATGD FAYAAKHAEV IHMGTYLPVR RARGENEPGG VPFGYLADIC QSSRVNYEDP 310 320 330 340 350 360 VRVSLDVVAT GAMLYDQIWL GSYMSGGVGF TQYATAAYTD NILDDFTYFG KEYVEDKYGL 370 380 390 400 410 420 CEAPNNMDTV LDVATEVTFY GLEQYEEYPA LLEDQFGGSQ RAAVVAAAAG CSTAFATGNA 430 440 450 460 470 480 QTGLSGWYLS MYLHKEQHSR LGFYGYDLQD QCGASNVFSI RGDEGLPLEL RGPNYPNYAM 490 500 510 520 530 540 NVGHQGEYAG ISQAPHAARG DAFVFNPLVK IAFADDNLVF DFTNVRGEFA KGALREFEPA 550 GERALITPAK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of the methyl coenzyme M reductase genes from Methanobacterium thermoautotrophicum." Bokranz M., Baeumner G., Allmansberger R., Ankel-Fuchs D., Klein A. J. Bacteriol. 170:568-577(1988) [PubMed: 2448287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg.
[2]	"Complete genome sequence of Methanothermobacter marburgensis, a methanoarchaeon model organism." Liesegang H., Kaster A.K., Wiezer A., Goenrich M., Wollherr A., Seedorf H., Gottschalk G., Thauer R.K. J. Bacteriol. 192:5850-5851(2010) [PubMed: 20802048] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg.
[3]	"Two genetically distinct methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum strain Marburg and delta H." Rospert S., Linder D., Ellermann J., Thauer R.K. Eur. J. Biochem. 194:871-877(1990) [PubMed: 2269306] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-19. Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg.
[4]	"The biosynthesis of methylated amino acids in the active site region of methyl-coenzyme M reductase." Selmer T., Kahnt J., Goubeaud M., Shima S., Grabarse W., Ermler U., Thauer R.K. J. Biol. Chem. 275:3755-3760(2000) [PubMed: 10660523] [Abstract] Cited for: POST-TRANSLATIONAL MODIFICATIONS. Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg.
[5]	"Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation." Ermler U., Grabarse W., Shima S., Goubeaud M., Thauer R.K. Science 278:1457-1462(1997) [PubMed: 9367957] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS). Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg.
[6]	"On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding." Grabarse W., Mahlert F., Duin E.C., Goubeaud M., Shima S., Thauer R.K., Lamzin V., Ermler U. J. Mol. Biol. 309:315-330(2001) [PubMed: 11491299] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.16 ANGSTROMS). Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X07794 Genomic DNA. Translation: CAA30639.1.
CP001710 Genomic DNA. Translation: ADL59127.1.

RefSeq

YP_003850440.1. NC_014408.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HBM	X-ray	1.80	A/D	2-550	[»]
1HBN	X-ray	1.16	A/D	2-550	[»]
1HBO	X-ray	1.78	A/D	2-550	[»]
1HBU	X-ray	1.90	A/D	2-550	[»]
1MRO	X-ray	1.16	A/D	2-549	[»]
3M1V	X-ray	1.45	A/D	2-550	[»]
3M2R	X-ray	1.30	A/D	2-550	[»]
3M2U	X-ray	1.40	A/D	2-550	[»]
3M2V	X-ray	1.80	A/D	2-550	[»]
3M30	X-ray	1.45	A/D	2-550	[»]
3M32	X-ray	1.35	A/D	2-550	[»]
3POT	X-ray	1.20	A/D	1-550	[»]

ProteinModelPortal

P11558.

SMR

P11558. Positions 2-549.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

9705257.

GenomeReviews

Gene locus MTBMA_c15480 in contig CP001710_GR.

KEGG

mmg:MTBMA_c15480.

Organism-specific databases

CMR

Search...

Phylogenomic databases

OMA

MSMISAY.

ProtClustDB

CLSK876061.

Family and domain databases

InterPro

IPR022681. MCR_a/b_chain_a-bundle.
IPR016212. Me_CoM_Rdtase_asu.
IPR008924. Me_CoM_Rdtase_asu/bsu_C.
IPR009047. Me_CoM_Rdtase_asu_C.
IPR003183. Me_CoM_Rdtase_asu_N.
IPR015811. Me_CoM_Rdtase_asu_N_sub1.
IPR015823. Me_CoM_Rdtase_asu_N_sub2.
IPR009024. Me_CoM_Rdtase_Fd-like_fold.
[Graphical view]

Gene3D

G3DSA:1.20.840.10. MCR_a/b_chain_a-bundle. 1 hit.
G3DSA:3.90.390.10. Me_CoM_Rdtase_asu_N_sub1. 1 hit.
G3DSA:3.30.70.470. Me_CoM_Rdtase_asu_N_sub2. 1 hit.

KO

K00399.

Pfam

PF02249. MCR_alpha. 1 hit.
PF02745. MCR_alpha_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000262. MCR_alpha. 1 hit.

SUPFAM

SSF48081. MCR_alpha_beta_C. 1 hit.
SSF55088. MCR_fer_like. 1 hit.

TIGRFAMs

TIGR03256. Met_CoM_red_alp. 1 hit.

ProtoNet

Search...

Entry information

Entry name

MCRA_METTM

Accession

Primary (citable) accession number: P11558
Secondary accession number(s): D9PY29

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 91 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program