P94951 (MTD_METKA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
F420-dependent methylenetetrahydromethanopterin dehydrogenase
Short name=MTD
EC=1.5.99.9

Alternative name(s):
Coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase

Gene names

Name:	mtd
Ordered Locus Names:	MK0011

Organism

Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)

Taxonomic identifier

190192 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanopyri › Methanopyrales › Methanopyraceae › Methanopyrus

Protein attributes

Sequence length	283 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	Catalyzes the reversible reduction of methenyl-H4MPT+ to methylene-H4MPT. Ref.1
Catalytic activity	5,10-methylenetetrahydromethanopterin + coenzyme F420 = 5,10-methenyltetrahydromethanopterin + reduced coenzyme F420. HAMAP MF_00058
Enzyme regulation	Strictly dependent on the presence of salts for activity. HAMAP MF_00058
Pathway	One-carbon metabolism; methanogenesis from CO(2); 5,10-methylene-5,6,7,8-tetrahydromethanopterin from 5,10-methenyl-5,6,7,8-tetrahydromethanopterin (coenzyme F420 route): step 1/1. HAMAP MF_00058
Subunit structure	Homohexamer composed of a trimer of dimers.
Sequence similarities	Belongs to the MTD family.
Biophysicochemical properties	Temperature dependence: Optimum temperature is 75 degrees Celsius. HAMAP MF_00058

Ontologies

Keywords
Biological process	Methanogenesis One-carbon metabolism
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	methanogenesis Inferred from electronic annotation. Source: UniProtKB-KW one-carbon metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ferredoxin hydrogenase activity Inferred from electronic annotation. Source: InterPro methylenetetrahydromethanopterin dehydrogenase activity Inferred from electronic annotation. Source: EC
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 – 283

282

F420-dependent methylenetetrahydromethanopterin dehydrogenase HAMAP MF_00058

PRO_0000075039

Experimental info

Sequence conflict

11

1

C → E AA sequence Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

283

Helix Strand Turn

Details...

Beta strand

4 – 10

7

Helix

15 – 19

5

Helix

22 – 24

3

Beta strand

31 – 39

9

Helix

46 – 63

18

Beta strand

66 – 71

6

Helix

78 – 88

11

Beta strand

90 – 92

3

Beta strand

94 – 99

6

Helix

100 – 105

6

Helix

106 – 111

6

Beta strand

115 – 119

5

Turn

129 – 131

3

Helix

134 – 150

17

Helix

153 – 169

17

Helix

175 – 177

3

Beta strand

180 – 183

4

Helix

185 – 190

6

Helix

197 – 222

26

Helix

227 – 257

31

Sequences

	Sequence		Length	Mass (Da)
	P94951 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: D2B778CB34D3034C	FASTA	283	31,382
	10 20 30 40 50 60 MTVAKAIFIK CGNLGTSMMM DMLLDERADR EDVEFRVVGT SVKMDPECVE AAVEMALDIA 70 80 90 100 110 120 EDFEPDFIVY GGPNPAAPGP SKAREMLADS EYPAVIIGDA PGLKVKDEME EQGLGYILVK 130 140 150 160 170 180 PDAMLGARRE FLDPVEMAIY NADLMKVLAA TGVFRVVQEA FDELIEKAKE DEISENDLPK 190 200 210 220 230 240 LVIDRNTLLE REEFENPYAM VKAMAALEIA ENVADVSVEG CFVEQDKERY VPIVASAHEM 250 260 270 280 MRKAAELADE ARELEKSNDA VLRTPHAPDG KVLSKRKFME DPE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Overexpression of the coenzyme-F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase gene from the hyperthermophilic Methanopyrus kandleri." Klein A.R., Thauer R.K. Eur. J. Biochem. 245:386-391(1997) [PubMed: 9151968] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens." Slesarev A.I., Mezhevaya K.V., Makarova K.S., Polushin N.N., Shcherbinina O.V., Shakhova V.V., Belova G.I., Aravind L., Natale D.A., Rogozin I.B., Tatusov R.L., Wolf Y.I., Stetter K.O., Malykh A.G., Koonin E.V., Kozyavkin S.A. Proc. Natl. Acad. Sci. U.S.A. 99:4644-4649(2002) [PubMed: 11930014] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.
[3]	"Two N5,N10-methylenetetrahydromethanopterin dehydrogenases in the extreme thermophile Methanopyrus kandleri: characterization of the coenzyme F420-dependent enzyme." Klein A.R., Koch J., Stetter K.O., Thauer R.K. Arch. Microbiol. 160:186-192(1993) [PubMed: 8215796] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-35, CHARACTERIZATION. Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.
[4]	"Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms." Hagemeier C.H., Shima S., Warkentin E., Thauer R.K., Ermler U. Acta Crystallogr. D 59:1653-1655(2003) [PubMed: 12925803] [Abstract] Cited for: CRYSTALLIZATION.
[5]	"Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure." Hagemeier C.H., Shima S., Thauer R.K., Bourenkov G., Bartunik H.D., Ermler U. J. Mol. Biol. 332:1047-1057(2003) [PubMed: 14499608] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y10251 Genomic DNA. Translation: CAA71298.1.
AE009439 Genomic DNA. Translation: AAM01228.1.

RefSeq

NP_613298.1. NC_003551.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QV9	X-ray	1.54	A/B/C	1-283	[»]
1U6I	X-ray	2.20	A/B/C/D/E/F/G/H/I/J/K/L	2-282	[»]
1U6J	X-ray	2.40	A/B/C/D/E/F/G/H/I/J/K/L	2-282	[»]
1U6K	X-ray	1.55	A/B/C	2-282	[»]
3IQE	X-ray	1.80	A/B/C/D/E/F	1-283	[»]
3IQF	X-ray	2.10	A/B/C/D/E/F/G/H/I/J/K/L	1-283	[»]
3IQZ	X-ray	2.10	A/B/C/D/E/F	1-283	[»]

ProteinModelPortal

P94951.

SMR

P94951. Positions 2-283.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1477313.

GenomeReviews

Gene locus MK0011 in contig AE009439_GR.

KEGG

mka:MK0011.

NMPDR

fig|190192.1.peg.11.

Phylogenomic databases

HOGENOM

HBG538567.

OMA

NPYAKAK.

ProtClustDB

PRK00994.

Enzyme and pathway databases

BioCyc

MKAN190192:MK0011-MONOMER.

Family and domain databases

HAMAP

MF_00058. MTD.
[Tree]

InterPro

IPR002844. Methylene_DH.
[Graphical view]

KO

K00319.

Pfam

PF01993. MTD. 1 hit.
[Graphical view]

PIRSF

PIRSF005627. MTD. 1 hit.

ProDom

PD017604. Methylene_DH. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF102324. MeTD. 1 hit.

ProtoNet

Search...

Entry information

Entry name

MTD_METKA

Accession

Primary (citable) accession number: P94951
Secondary accession number(s): Q9UWL4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2007
Last modified:	November 16, 2011
This is version 84 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program