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(-) Description

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 :  1.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
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
PubMed-ID: 20707311  |  Reference-DOI: 10.1021/BI100458D

(-) Compounds

Molecule 1 - METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA
    Chains: A, D
    EC Number: 2.8.4.1
    Organism Scientific: METHANOTHERMOBACTER MARBURGENSIS
    Organism Taxid: 79929
    Strain: MARBURG / DSM 2133
    Synonym: MCR I ALPHA, COENZYME-B SULFOETHYLTHIOTRANSFERASE ALPHA
 
Molecule 2 - METHYL-COENZYME M REDUCTASE I SUBUNIT BETA
    Chains: B, E
    EC Number: 2.8.4.1
    Organism Scientific: METHANOTHERMOBACTER MARBURGENSIS
    Organism Taxid: 79929
    Strain: MARBURG / DSM 2133
    Synonym: MCR I BETA, COENZYME-B SULFOETHYLTHIOTRANSFERASE BETA
 
Molecule 3 - METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA
    Chains: C, F
    EC Number: 2.8.4.1
    Organism Scientific: METHANOTHERMOBACTER MARBURGENSIS
    Organism Taxid: 79929
    Strain: MARBURG / DSM 2133
    Synonym: MCR I GAMMA, COENZYME-B SULFOETHYLTHIOTRANSFERASE GAMMA

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (14, 41)

Asymmetric/Biological Unit (14, 41)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AGM2Mod. Amino Acid5-METHYL-ARGININE
3COM2Ligand/Ion1-THIOETHANESULFONIC ACID
4EDO7Ligand/Ion1,2-ETHANEDIOL
5F432Ligand/IonFACTOR 430
6GL32Mod. Amino AcidTHIOGLYCIN
7MG11Ligand/IonMAGNESIUM ION
8MGN2Mod. Amino Acid2-METHYL-GLUTAMINE
9MHS2Mod. Amino AcidN1-METHYLATED HISTIDINE
10PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
11SMC2Mod. Amino AcidS-METHYLCYSTEINE
12TP72Ligand/IonCOENZYME B
13TXZ2Ligand/IonO-PHOSPHONO-N-(6-SULFANYLHEXANOYL)-L-THREONINE
14ZN1Ligand/IonZINC ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREACT A:556 , HOH A:713 , HOH A:1599 , HOH A:2285 , HOH A:3828 , HOH A:3971BINDING SITE FOR RESIDUE MG A 551
02AC2SOFTWAREGLU A:20 , HOH A:657 , HOH A:1164 , HOH A:3761 , HOH A:4216 , HOH A:4217BINDING SITE FOR RESIDUE MG A 552
03AC3SOFTWAREALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:652 , HOH A:675 , HOH A:677 , HOH A:697 , HOH A:699 , HOH A:788 , HOH A:4193 , 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:555 , HOH D:666 , 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:582BINDING SITE FOR RESIDUE F43 A 1
04AC4SOFTWAREARG A:270 , LEU A:320 , MET A:324 , SER A:325 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:592 , HOH A:607 , HOH A:621 , HOH A:685 , HOH A:3684 , PHE B:362 , TYR B:367 , GLY B:368 , GLY B:369 , HIS B:379 , ILE B:380 , ARG D:225 , LYS D:256 , MHS D:257BINDING SITE FOR RESIDUE TP7 A 553
05AC5SOFTWARETYR A:333 , PHE A:443 , TYR A:444 , HOH A:3682 , HOH A:4190 , HOH A:4191 , HOH A:4192 , HOH A:4194 , PHE B:361 , SER B:365 , TYR B:367 , LEU C:117 , ARG C:120 , F43 D:553BINDING SITE FOR RESIDUE COM A 554
06AC6SOFTWAREARG A:270 , MET A:324 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:592 , HOH A:607 , HOH A:621 , HOH A:685 , HOH A:3684 , PHE B:362 , GLY B:368 , GLY B:369 , HIS B:379 , ILE B:380 , ARG D:225 , LYS D:256 , MHS D:257BINDING SITE FOR RESIDUE TXZ A 555
07AC7SOFTWAREVAL A:519 , LYS A:531 , PHE A:537 , GLU A:538 , MG A:551 , HOH A:642 , HOH A:713 , HOH A:1396 , HOH A:2285 , HOH A:3828 , HOH A:3971 , HOH A:3988BINDING SITE FOR RESIDUE ACT A 556
08AC8SOFTWARETYR A:348BINDING SITE FOR RESIDUE EDO A 557
09AC9SOFTWAREASN A:110 , HIS A:111BINDING SITE FOR RESIDUE EDO A 558
10BC1SOFTWAREALA A:48 , HOH A:4212 , LYS B:7BINDING SITE FOR RESIDUE PEG A 559
11BC2SOFTWAREARG A:102 , SER A:215 , ARG A:216 , CYS A:218 , ARG D:102 , SER D:215 , ARG D:216 , CYS D:218BINDING SITE FOR RESIDUE ZN A 560
12BC3SOFTWAREHOH B:1305 , HOH B:3547 , HOH B:3548 , HOH B:3549 , HOH B:3550 , HOH B:3714BINDING SITE FOR RESIDUE MG B 444
13BC4SOFTWAREASP B:271 , HOH B:564 , HOH B:811 , HOH B:1206 , HOH B:3076 , HOH B:4127BINDING SITE FOR RESIDUE MG B 445
14BC5SOFTWAREGLU C:30 , HOH C:1095 , HOH C:3555 , HOH C:3556 , HOH C:3557 , HOH C:3558BINDING SITE FOR RESIDUE MG C 250
15BC6SOFTWARELYS C:153 , HOH C:1067BINDING SITE FOR RESIDUE ACT C 1
16BC7SOFTWAREARG C:236 , HOH C:856 , HOH C:3762BINDING SITE FOR RESIDUE EDO C 251
17BC8SOFTWAREARG C:43 , GLY C:46 , GLU C:47 , GLU C:48 , TYR C:49 , HOH C:3630BINDING SITE FOR RESIDUE PEG C 252
18BC9SOFTWAREHOH D:3543 , HOH D:3544 , HOH D:3546 , HOH F:3542 , HOH F:3545BINDING SITE FOR RESIDUE MG D 1
19CC1SOFTWAREHOH D:1116 , HOH D:3559 , HOH D:3560 , HOH D:3561 , HOH D:3562 , HOH D:3563BINDING SITE FOR RESIDUE MG D 551
20CC2SOFTWAREGLU D:175 , HOH D:4000 , HOH D:4001 , HOH D:4183BINDING SITE FOR RESIDUE MG D 552
21CC3SOFTWAREGLY 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:554 , HOH A:600 , HOH A:4194 , 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:647 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243 , HOH D:571 , HOH D:647 , HOH D:670 , HOH D:713 , HOH D:721 , HOH D:723BINDING SITE FOR RESIDUE F43 D 553
22CC4SOFTWAREARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:570 , HOH D:575 , HOH D:583 , HOH D:632 , HOH D:664 , PHE E:362 , TYR E:367 , GLY E:368 , GLY E:369 , HIS E:379 , ILE E:380BINDING SITE FOR RESIDUE TP7 D 554
23CC5SOFTWAREF43 A:1 , HOH A:4189 , HOH A:4193 , TYR D:333 , PHE D:443 , TYR D:444 , HOH D:760 , PHE E:361 , SER E:365 , TYR E:367 , LEU F:117 , ARG F:120 , HOH F:4187 , HOH F:4188BINDING SITE FOR RESIDUE COM D 555
24CC6SOFTWAREARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , MET D:324 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:570 , HOH D:575 , HOH D:583 , HOH D:632 , HOH D:664 , PHE E:362 , GLY E:368 , GLY E:369 , HIS E:379 , ILE E:380BINDING SITE FOR RESIDUE TXZ D 556
25CC7SOFTWARETYR D:348BINDING SITE FOR RESIDUE EDO D 557
26CC8SOFTWARELYS D:22 , ARG F:147 , GLY F:166 , GLU F:207BINDING SITE FOR RESIDUE EDO D 558
27CC9SOFTWAREHOH E:2200 , HOH E:2328 , HOH E:3583 , HOH E:3584 , HOH E:3585BINDING SITE FOR RESIDUE MG E 444
28DC1SOFTWAREASP E:271 , HOH E:1466 , HOH E:1684 , HOH E:3695 , HOH E:4090BINDING SITE FOR RESIDUE MG E 445
29DC2SOFTWAREGLU F:30 , HOH F:1294 , HOH F:3551 , HOH F:3552 , HOH F:3553 , HOH F:3554BINDING SITE FOR RESIDUE MG F 250
30DC3SOFTWARELYS F:132 , HOH F:1243BINDING SITE FOR RESIDUE EDO F 251
31DC4SOFTWAREHOH F:832BINDING SITE FOR RESIDUE EDO F 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M2U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr B:164 -Pro B:165
2Tyr E:164 -Pro E:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M2U)

(-) Exons   (0, 0)

(no "Exon" information available for 3M2U)

(-) Sequences/Alignments

Asymmetric/Biological 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:548
 aligned with MCRA_METTM | P11558 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:548
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541        
           MCRA_METTM     2 ADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKHAEVIHMGTYLPVRRARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSQRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYGYDLQDQCGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPA 549
               SCOP domains d3m2ua1 A:2-269 Alpha chain                                                                                                                                                                                                                                                 d3m2ua2 A:270-549 Alpha chain                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh..................eee......eee.hhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....................eeeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..ee......hhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............hhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhh...hhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhh..........hhhhhhhhhhh........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m2u A   2 ADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKhAEVIHMGTYLPVRrARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSqRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYgYDLQDQcGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPA 549
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     | 261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441   |   451|      461       471       481       491       501       511       521       531       541        
                                                                                                                                                                                                                                                                                         257-MHS       271-AGM                                                                                                                          400-MGN                                      445-GL3  |                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            452-SMC                                                                                             


Chain B from PDB  Type:PROTEIN  Length:442
 aligned with MCRB_METTM | P11560 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:442
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441  
           MCRB_METTM     2 AKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI 443
               SCOP domains d3m2ub1 B:2-188 Beta chain                                                                                                                                                                 d3m2ub2 B:189-443 Beta chain                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeeeee.hhhh...hhhhhhhhhhhhheeeehhhhhhhhhhhh....................hhhhhhhhhhhhhh.......eeeeehhhheeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh............ee....hhhhh....hhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeee..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhh.............hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m2u B   2 AKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI 443
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441  


Chain C from PDB  Type:PROTEIN  Length:246
 aligned with MCRG_METTM | P11562 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
           MCRG_METTM     2 AQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFN 247
               SCOP domains d3m2uc_ C: Methyl-coenzyme M reductase gamma chain                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...........hhhhhhhhhh.............hhhhh....hhhhhhh..hhhhhhh..eeeeeeee.......hhhhhhhhhhhhh...eeee....eeeeeehhhhhhhhhhhhhh.......eee........................eee......eeeee.....eeeeeee.....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m2u C   2 AQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFN 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain D from PDB  Type:PROTEIN  Length:548
 aligned with MCRA_METTM | P11558 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:548
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541        
           MCRA_METTM     2 ADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKHAEVIHMGTYLPVRRARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSQRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYGYDLQDQCGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPA 549
               SCOP domains d3m2ud1 D:2-269 Alpha chain                                                                                                                                                                                                                                                 d3m2ud2 D:270-549 Alpha chain                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MCR_alpha_N-3m2uD03 D:2-268                                                                                                                                                                                                                                                -----------------------------------------------MCR_alpha-3m2uD01 D:316-441                                                                                                   ------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) MCR_alpha_N-3m2uD04 D:2-268                                                                                                                                                                                                                                                -----------------------------------------------MCR_alpha-3m2uD02 D:316-441                                                                                                   ------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh..................eee......eee.hhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....................eeeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..ee......hhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh............hhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhh...hhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhh..........hhhhhhhhhhh........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m2u D   2 ADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKhAEVIHMGTYLPVRrARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSqRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYgYDLQDQcGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPA 549
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     | 261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441   |   451|      461       471       481       491       501       511       521       531       541        
                                                                                                                                                                                                                                                                                         257-MHS       271-AGM                                                                                                                          400-MGN                                      445-GL3  |                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            452-SMC                                                                                             


Chain E from PDB  Type:PROTEIN  Length:442
 aligned with MCRB_METTM | P11560 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:442
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441  
           MCRB_METTM     2 AKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI 443
               SCOP domains d3m2ue1 E:2-188 Beta chain                                                                                                                                                                 d3m2ue2 E:189-443 Beta chain                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----MCR_beta_N-3m2uE03 E:6-187                                                                                                                                                            -MCR_beta-3m2uE01 E:189-442                                                                                                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) ----MCR_beta_N-3m2uE04 E:6-187                                                                                                                                                            -MCR_beta-3m2uE02 E:189-442                                                                                                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author .....eeeee.....eeeeeee.hhhh...hhhhhhhhhhhhheeeehhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.......eeeeehhhheeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh............ee....hhhhh....hhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeee..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhh.............hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m2u E   2 AKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI 443
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441  


Chain F from PDB  Type:PROTEIN  Length:246
 aligned with MCRG_METTM | P11562 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
           MCRG_METTM     2 AQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFN 247
               SCOP domains d3m2uf_ F: Methyl-coenzyme M reductase gamma chain                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) MCR_gamma-3m2uF01 F:2-247                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) MCR_gamma-3m2uF02 F:2-247                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhh...........hhhhhhhhhh.............hhhhhh...hhhhhhh..hhhhhhh..eeeeeeee.......hhhhhhhhhhhhh...eeee....eeeeeehhhhhhhhhhhhhh.......eee........................eeee....eeeeee.....eeeeeee.....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m2u F   2 AQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFN 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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  (5, 10)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M2U)

(-) Pfam Domains  (5, 10)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MCR_alpha] (8)
(-)
Clan: no clan defined [family: MCR_alpha_N] (8)
(-)
Clan: no clan defined [family: MCR_beta] (8)
(-)
Clan: no clan defined [family: MCR_beta_N] (8)
(-)
Clan: no clan defined [family: MCR_gamma] (8)

(-) Gene Ontology  (4, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D   (MCRA_METTM | P11558)
molecular function
    GO:0050524    coenzyme-B sulfoethylthiotransferase activity    Catalysis of the reaction: coenzyme B + methyl-coenzyme M = coenzyme M-coenzyme B heterodisulfide + methane. Methyl-CoM is also known as 2-(methylthio)ethanesulfonate, coenzyme B as N-(7-mercaptoheptanoyl)threonine 3-O-phosphate, and coenzyme M-coenzyme B heterodisulfide as CoM-S-S-CoB.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.

Chain B,E   (MCRB_METTM | P11560)
molecular function
    GO:0050524    coenzyme-B sulfoethylthiotransferase activity    Catalysis of the reaction: coenzyme B + methyl-coenzyme M = coenzyme M-coenzyme B heterodisulfide + methane. Methyl-CoM is also known as 2-(methylthio)ethanesulfonate, coenzyme B as N-(7-mercaptoheptanoyl)threonine 3-O-phosphate, and coenzyme M-coenzyme B heterodisulfide as CoM-S-S-CoB.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.

Chain C,F   (MCRG_METTM | P11562)
molecular function
    GO:0050524    coenzyme-B sulfoethylthiotransferase activity    Catalysis of the reaction: coenzyme B + methyl-coenzyme M = coenzyme M-coenzyme B heterodisulfide + methane. Methyl-CoM is also known as 2-(methylthio)ethanesulfonate, coenzyme B as N-(7-mercaptoheptanoyl)threonine 3-O-phosphate, and coenzyme M-coenzyme B heterodisulfide as CoM-S-S-CoB.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCRA_METTM | P11558: 1hbm 1hbn 1hbo 1hbu 1mro 3m1v 3m2r 3m2v 3m30 3m32 3pot 5a0y 5g0r
        MCRB_METTM | P11560: 1hbm 1hbn 1hbo 1hbu 1mro 3m1v 3m2r 3m2v 3m30 3m32 3pot 5a0y 5g0r
        MCRG_METTM | P11562: 1hbm 1hbn 1hbo 1hbu 1mro 3m1v 3m2r 3m2v 3m30 3m32 3pot 5a0y 5g0r

(-) Related Entries Specified in the PDB File

3m1v 3m2r 3m2v 3m30 3m32