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(-) Description

Title :  METHANE MONOOXYGENASE HYDROXYLASE
 
Authors :  N. Elango, R. Radhakrishnan, W. A. Froland, B. J. Waller, C. A. Earhart, J. D. Lipscomb, D. H. Ohlendorf
Date :  21 Oct 96  (Deposition) - 15 May 97  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  B,D,G
Biol. Unit 1:  B,D,G  (2x)
Keywords :  Oxidoreductase, Monooxygenase, Nadp, One-Carbon Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Elango, R. Radhakrishnan, W. A. Froland, B. J. Wallar, C. A. Earhart J. D. Lipscomb, D. H. Ohlendorf
Crystal Structure Of The Hydroxylase Component Of Methane Monooxygenase From Methylosinus Trichosporium Ob3B
Protein Sci. V. 6 556 1997
PubMed-ID: 9070438

(-) Compounds

Molecule 1 - METHANE MONOOXYGENASE HYDROXYLASE
    Chains: B
    EC Number: 1.14.13.25
    Organism Scientific: METHYLOSINUS TRICHOSPORIUM
    Organism Taxid: 426
 
Molecule 2 - METHANE MONOOXYGENASE HYDROXYLASE
    Chains: D
    EC Number: 1.14.13.25
    Organism Scientific: METHYLOSINUS TRICHOSPORIUM
    Organism Taxid: 426
 
Molecule 3 - METHANE MONOOXYGENASE HYDROXYLASE
    Chains: G
    EC Number: 1.14.13.25
    Organism Scientific: METHYLOSINUS TRICHOSPORIUM
    Organism Taxid: 426

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : BDG
Biological Unit 1 (2x): BDG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU D:114 , GLU D:144 , HIS D:147 , FE D:802 , HOH D:803 , HOH D:804 , HOH D:805BINDING SITE FOR RESIDUE FE D 801
2AC2SOFTWAREGLU D:144 , GLU D:209 , GLU D:243 , HIS D:246 , FE D:801 , HOH D:803 , HOH D:804BINDING SITE FOR RESIDUE FE D 802
3FE2UNKNOWNFE D:801 , FE D:802 , HOH D:803 , HOH D:804 , HOH D:805 , GLU D:114 , GLU D:144 , GLU D:209 , GLU D:243 , HIS D:147 , HIS D:246THE PROPOSED ACTIVE SITE FOR THIS ENZYME CONSISTS OF BIS-MU-OXO BRIDGED DIIRONS LIGATED TO RESIDUES D 114, D 144, D 147, D 209, D 243, D 246, HOH1, HOH 2, AND HOH 3.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MHY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro G:121 -Pro G:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MHY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MHY)

(-) Exons   (0, 0)

(no "Exon" information available for 1MHY)

(-) 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 B from PDB  Type:PROTEIN  Length:383
 aligned with MEMB_METTR | P27354 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:383
                                                                                                                                                                                                                                                                                                                                                                                                    372                    
                                                                                                                                                                                                                                                                                                                                                                                                  371 |                    
                                    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       350       360       370| |    379       389   
           MEMB_METTR    11 KRGLTDPERAAIIAAAVPDHALDTQRKYHYFIQPRWKPLSEYEQLSCYAQPNPDWIAGGLDWGDWTQKFHGGRPSWGNESTELRTTDWYRHRDPARRWHHPYVKDKSEEARYTQRFLAAYSSEGSIRTIDPYWRDEILNKYFGALLYSEYGLFNAHSSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYSGARATVQEIWQGVQDWNEILWAGHAVMIATFGQFARREFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDSEFGAHNRTFLNAWTEHYLASSVAALKDFVGLYAKVEKSRADRSRRRLRGAAASSAIGRSIT-PDKIGFRVDVDQKVDAVLAGY 392
               SCOP domains d1mhyb_ B: Methane monooxygenase hydrolase beta subunit                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1mhyB00 B:11-393 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------Phenol_Hydrox-1mhyB01 B:74-311                                                                                                                                                                                                                ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh........................hhhhhh....................................................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mhy B  11 KRGLTDPERAAIIAAAVPDHALDTQRKYHYFIQPRWKPLSEYEQLSCYAQPNPDWIAGGLDWGDWTQKFHGGRPSWGNESTELRTTDWYRHRDPARRWHHPYVKDKSEEARYTQRFLAAYSSEGSIRTIDPYWRDEILNKYFGALLYSEYGLFNAHSSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYSGARATVQEIWQGVQDWNEILWAGHAVYDATFGQFARREFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDSEFGAHNRTFLNAWTEHYLASSVAALKDFVGLYAKVEKVAGATDSAGVSEALQRVFGDWKIDYADKIGFRVDVDQKVDAVLAGY 393
                                    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       350       360       370       380       390   


Chain D from PDB  Type:PROTEIN  Length:510
 aligned with MEMA_METTR | P27353 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:510
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526
           MEMA_METTR    17 NRAPVGVEPQEVHKWLQSFNWDFKENRTKYPTKYHMANETKEQFKVIAKEYARMEAAKDERQFGTLLDGLTRLGAGNKVHPRWGETMKVISNFLEVGEYNAIAASAMLWDSATAAEQKNGYLAQVLDEIRHTHQCAFINHYYSKHYHDPAGHNDARRTRAIGPLWKGMKRVFADGFISGDAVECSVNLQLVGEACFTNPLIVAVTEWASANGDEITPTVFLSVETDELRHMANGYQTVVSIANDPASAKFLNTDLNNAFWTQQKYFTPVLGYLFEYGSKFKVEPWVKTWNRWVYEDWGGIWIGRLGKYGVESPASLRDAKRDAYWAHHDLALAAYAMWPLGFARLALPDEEDQAWFEANYPGWADHYGKIFNEWKKLGYEDPKSGFIPYQWLLANGHDVYIDRVSQVPFIPSLAKGTGSLRVHEFNGKKHSLTDDWGERQWLIEPERYECHNVFEQYEGRELSEVIAEGHGVRSDGKTLIAQPHTRGDNLWTLEDIKRAGCVFPDPLAKF 526
               SCOP domains d1mhyd_ D: Methane monooxygenase hydrolase alpha subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1mhyD00 D:17-526 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------Phenol_Hydrox-1mhyD01 D:36-263                                                                                                                                                                                                      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhh.............hhhhhhhhhh.......hhhhhhhhhh...........hhhhhhh..........................eeeee..eeeee..hhhhhhhhh.........hhhhh....hhhhhhh........................hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mhy D  17 NRAPVGVEPQEVHKWLQSFNWDFKENRTKYPTKYHMANETKEQFKVIAKEYARMEAAKDERQFGTLLDGLTRLGAGNKVHPRWGETMKVISNFLEVGEYNAIAASAMLWDSATAAEQKNGYLAQVLDEIRHTHQCAFINHYYSKHYHDPAGHNDARRTRAIGPLWKGMKRVFADGFISGDAVECSVNLQLVGEACFTNPLIVAVTEWASANGDEITPTVFLSVETDELRHMANGYQTVVSIANDPASAKFLNTDLNNAFWTQQKYFTPVLGYLFEYGSKFKVEPWVKTWNRWVSEDWGGIWIGRLGKYGVESPRSLRDAKRDAYWAHHDLALAAYAMWPLGFARLALPDEEDQAWFEANYPGWADHYGKIFNEWKKLGYEDPKSGFIPYQWLLANGHDVYIDRVSQVPFIPSLAKGTGSLRVHEFNGKKHSLTDDWGERQWLIEPERYECHNVFEQYEGRELSEVIAEGHGVRSDGKTLIAQPHTRGDNLWTLEDIKRAGCVFPDPLAKF 526
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526


Chain G from PDB  Type:PROTEIN  Length:167
 aligned with MEMG_METTR | P27355 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           MEMG_METTR     2 AKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDRAAVEATWIAKIKAAKSKYEADGIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKEPGVKVLHLQ 168
               SCOP domains d1mhyg_ G: Methane monooxygenase hydrolase, gamma subunit                                                                                                               SCOP domains
               CATH domains ---1mhyG01 G:5-72  [code=1.20.1280.10, no name defined]                1mhyG02 G:73-145  [code=1.20.1280.30, no name defined]                   ----------------------- CATH domains
               Pfam domains -----MeMO_Hyd_G-1mhyG01 G:7-167                                                                                                                                       - Pfam domains
         Sec.struct. author .........hhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mhy G   2 AKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIKAAKSKYEAEAIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQ 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (3, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: Ferritin (185)
(-)
Clan: no clan defined [family: MeMO_Hyd_G] (13)

(-) Gene Ontology  (9, 20)

Asymmetric Unit(hide GO term definitions)
Chain B   (MEMB_METTR | P27354)
molecular function
    GO:0015049    methane monooxygenase activity    Catalysis of the reaction: methane + NAD(P)H + H+ + O2 = methanol + NAD(P)+ + H2O.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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.
    GO:0016709    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

Chain D   (MEMA_METTR | P27353)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0015049    methane monooxygenase activity    Catalysis of the reaction: methane + NAD(P)H + H+ + O2 = methanol + NAD(P)+ + H2O.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

Chain G   (MEMG_METTR | P27355)
molecular function
    GO:0015049    methane monooxygenase activity    Catalysis of the reaction: methane + NAD(P)H + H+ + O2 = methanol + NAD(P)+ + H2O.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0015947    methane metabolic process    The chemical reactions and pathways involving methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MEMA_METTR | P27353: 1mhz
        MEMB_METTR | P27354: 1mhz
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(-) Related Entries Specified in the PDB File

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