3F47 - JenaLib

Title :   THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE (HMD) HOLOENZYME FROM METHANOCALDOCOCCUS JANNASCHII

Authors :   T. Hiromoto, O. Pilak, E. Warkentin, R. K. Thauer, S. Shima, U. Ermler

Date :   31 Oct 08 (Deposition) - 10 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Rossmann Fold, Helix Bundle, Complex With Iron Guanylyl Pyridinol Cofactor, Methanogenesis, One-Carbon Metabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hiromoto, K. Ataka, O. Pilak, S. Vogt, M. S. Stagni, W. Meyer-Klaucke, E. Warkentin, R. K. Thauer, S. Shima, U. Ermler
The Crystal Structure Of C176A Mutated [Fe]-Hydrogenase Suggests An Acyl-Iron Ligation In The Active Site Iron Complex.
Febs Lett. V. 583 585 2009
PubMed-ID: 19162018 | Reference-DOI: 10.1016/J.FEBSLET.2009.01.017
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:6 , GLY A:7 , GLY A:9 , CYS A:10 , THR A:13 , 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 , CYS A:176 , THR A:177 , PRO A:202 , FE2 A:360 , CMO A:361 , CMO A:362 , HOH A:364 , HOH A:373 , HOH A:385 , HOH A:404 , HOH A:471 , HOH A:487 , HOH A:493	BINDING SITE FOR RESIDUE I2C A 359
2	AC2	SOFTWARE	CYS A:176 , I2C A:359 , CMO A:361 , CMO A:362 , HOH A:364	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	BINDING SITE FOR RESIDUE CMO A 361
4	AC4	SOFTWARE	CYS A:176 , HIS A:201 , PRO A:202 , CYS A:204 , I2C A:359 , FE2 A:360 , CMO A:361 , HOH A:364	BINDING SITE FOR RESIDUE CMO A 362
5	AC5	SOFTWARE	LEU A:51 , VAL A:54 , PRO A:55 , VAL A:57	BINDING SITE FOR RESIDUE NA A 363

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:344
 aligned with HMD_METJA | Q58194 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
            HMD_METJA     1 MKIAILGAGCYRTHAAAGITNFMRACEVAKEVGKPEIALTHSSITYGAELLHLVPDVKEVIVSDPCFAEEPGLVVIDEFDPKEVMEAHLSGNPESIMPKIREVVKAKAKELPKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDLNITSYHPGCVPEMKGQVYIAEGYASEEAVNKLYEIGKIARGKAFKMPANLIGPVCDMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTADSMCFGPLAEILPTALKVLEKHKVVE 344
               SCOP domains d3f47a1 A:1-242 5,10-methenyltetrahydromethanopterin hydrogenase, HMD                                                                                                                                                                             d3f47a2 A:243-344 5,10-methenyltetrahydromethanopterin hydrogenase, HMD                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh..eeee....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......eeee..hhhhhh.eee.hhhhhhh...eeee......hhhhhhhhhhhhh....eeee....hhhhhhhhhhhh.....eeee............eeeee...hhhhhhhhhhhhhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f47 A   1 MKIAILGAGCYRTHAAAGITNFMRACEVAKEVGKPEIALTHSSITYGAELLHLVPDVKEVIVSDPCFAEEPGLVVIDEFDPKEVMEAHLSGNPESIMPKIREVVKAKAKELPKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDLNITSYHPGCVPEMKGQVYIAEGYASEEAVNKLYEIGKIARGKAFKMPANLIGPVCDMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTADSMCFGPLAEILPTALKVLEKHKVVE 344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (HMD_METJA | Q58194)

molecular function
	GO:0047068	N5,N10-methenyltetrahydromethanopterin hydrogenase activity	Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H(2) = 5,10-methylenetetrahydromethanopterin + H(+).
	GO:0018537	coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity	Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0015948	methanogenesis	The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
	GO:0019386	methanogenesis, from carbon dioxide	The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other compounds, including carbon dioxide (CO2).
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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