4AY8 - JenaLib

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Title :   SEMET-DERIVATIVE OF A METHYLTRANSFERASE FROM M. MAZEI

Authors :   A. Hoeppner, F. Thomas, A. Rueppel, R. Hensel, W. Blankenfeldt, P. Baye A. Faust

Date :   18 Jun 12 (Deposition) - 31 Oct 12 (Release) - 05 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Hoeppner, F. Thomas, A. Rueppel, R. Hensel, W. Blankenfeldt, P. Bayer, A. Faust
Structure Of The Corrinoid:Coenzyme M Methyltransferase Mtaa From Methanosarcina Mazei
Acta Crystallogr. , Sect. D V. 68 1549 2012
PubMed-ID: 23090404 | Reference-DOI: 10.1107/S090744491203853X

Molecule 1 - METHYLCOBALAMIN: COENZYME M METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.247
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	METHANOSARCINA MAZEI
	Organism Taxid	:	2209
	Synonym	:	CORRINOID COENZYME M METHYLTRANSFERASE MTAA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 31)

No.	Name	Count	Type	Full Name
1	COM	2	Ligand/Ion	1-THIOETHANESULFONIC ACID
2	CSD	2	Mod. Amino Acid	3-SULFINOALANINE
3	GOL	2	Ligand/Ion	GLYCEROL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	COM	1	Ligand/Ion	1-THIOETHANESULFONIC ACID
2	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 15)

No.	Name	Count	Type	Full Name
1	COM	1	Ligand/Ion	1-THIOETHANESULFONIC ACID
2	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
3	GOL	2	Ligand/Ion	GLYCEROL
4	MRD	-1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:31 , GLN A:32 , ARG A:73 , LEU A:78 , GLN A:97 , HIS A:240 , CYS A:242 , CYS A:319 , GLY A:320 , ZN A:600 , HOH A:2052	BINDING SITE FOR RESIDUE COM A 500
2	AC2	SOFTWARE	HIS A:240 , CYS A:242 , CYS A:319 , COM A:500	BINDING SITE FOR RESIDUE ZN A 600
3	AC3	SOFTWARE	LYS A:170 , LYS A:171 , THR A:172 , ASP A:173	BINDING SITE FOR RESIDUE MRD A 800
4	AC4	SOFTWARE	THR B:31 , GLN B:32 , ARG B:73 , LEU B:78 , GLN B:97 , CYS B:242 , CYS B:319 , GLY B:320 , ZN B:600 , HOH B:2051	BINDING SITE FOR RESIDUE COM B 500
5	AC5	SOFTWARE	HIS B:240 , CYS B:242 , CYS B:319 , COM B:500	BINDING SITE FOR RESIDUE ZN B 600
6	AC6	SOFTWARE	LYS B:170 , LYS B:171 , THR B:172 , ASP B:173	BINDING SITE FOR RESIDUE GOL B 700
7	AC7	SOFTWARE	PHE B:340	BINDING SITE FOR RESIDUE GOL B 701

(no "SS Bond" information available for 4AY8)

Asymmetric Unit

No.	Residues
1	Trp A:46	-	Pro A:47
2	Leu A:74	-	Pro A:75
3	Gly A:284	-	Asn A:285
4	Gly A:295	-	Pro A:296
5	Trp B:46	-	Pro B:47
6	Leu B:74	-	Pro B:75
7	Gly B:284	-	Asn B:285
8	Gly B:295	-	Pro B:296

(no "SAP(SNP)/Variant" information available for 4AY8)

(no "PROSITE Motif" information available for 4AY8)

(no "Exon" information available for 4AY8)

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:340
 aligned with Q8PXZ6_METMA | Q8PXZ6 from UniProtKB/TrEMBL  Length:342

    Alignment length:340
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
         Q8PXZ6_METMA     3 DMSEFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELMDVVGAPWPEAHTNPELMAKLALANHELSGLEAVRLPYCLTVLVEAMGCEINMGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGMEGPVTVASDLVSVKSFMKWSIKKTDLLEQALDIATEASIIYANAMVEAGADVIAIADPVASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPMTPLENVKALVAARDEFYA 342
               SCOP domains d4ay8a_ A: automated matches                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhh..eee........eeee..............hhhhh.hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhh....hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eee.hhhhhhhhhhhhhhh...eeeeeehhhhhhh..hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ay8 A   3 DmSEFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELmDVVGAPWPEAHTNPELmAKLALANHELSGLEAVRLPYcLTVLVEAmGCEINmGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGmEGPVTVASDLVSVKSFmKWSIKKTDLLEQALDIATEASIIYANAmVEAGADVIAIADPVASPDLmSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDmADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPmTPLENVKALVAARDEFYA 342
                             |      12        22        32      | 42        52   |    62        72    |   82  |     92       102       112       122       132       142     | 152       162  |    172       182       192|      202       212|      222       232       242       252       262       272       282       292       302       312       322 |     332       342
                             |                                 39-MSE           56-MSE               77-CSD  85-MSE |                                                      148-MSE          165-MSE                     193-MSE             213-MSE                                252-MSE                                                                 324-MSE              
                             4-MSE                                                                                 91-MSE

Chain B from PDB  Type:PROTEIN  Length:340
 aligned with Q8PXZ6_METMA | Q8PXZ6 from UniProtKB/TrEMBL  Length:342

    Alignment length:340
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
         Q8PXZ6_METMA     3 DMSEFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELMDVVGAPWPEAHTNPELMAKLALANHELSGLEAVRLPYCLTVLVEAMGCEINMGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGMEGPVTVASDLVSVKSFMKWSIKKTDLLEQALDIATEASIIYANAMVEAGADVIAIADPVASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPMTPLENVKALVAARDEFYA 342
               SCOP domains d4ay8b_ B: automated matches                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhh..eee........eeee..............hhhhh.hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhh....hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eee.hhhhhhhhhhhhhhh...eeeeeehhhhhhh..hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ay8 B   3 DmSEFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELmDVVGAPWPEAHTNPELmAKLALANHELSGLEAVRLPYcLTVLVEAmGCEINmGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGmEGPVTVASDLVSVKSFmKWSIKKTDLLEQALDIATEASIIYANAmVEAGADVIAIADPVASPDLmSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDmADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPmTPLENVKALVAARDEFYA 342
                             |      12        22        32      | 42        52   |    62        72    |   82  |     92       102       112       122       132       142     | 152       162  |    172       182       192|      202       212|      222       232       242       252       262       272       282       292       302       312       322 |     332       342
                             4-MSE                             39-MSE           56-MSE               77-CSD  85-MSE |                                                      148-MSE          165-MSE                     193-MSE             213-MSE                                252-MSE                                                                 324-MSE              
                                                                                                                   91-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: UROD/MetE-like (30)

Family: automated matches (4)

Protein domain: automated matches (4)

Methanosarcina mazei [TaxId: 2209] (2)

1a	d4ay8a_	A:
1b	d4ay8b_	B:

(no "CATH Domain" information available for 4AY8)

(no "Pfam Domain" information available for 4AY8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8PXZ6_METMA | Q8PXZ6)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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.
	GO:0004853	uroporphyrinogen decarboxylase activity	Catalysis of the reaction: uroporphyrinogen-III = coproporphyrinogen + 4 CO2.
biological process
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0006779	porphyrin-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

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	Cis Peptide Bonds
		Gly A:284 - Asn A:285	[ RasMol ]
		Gly A:295 - Pro A:296	[ RasMol ]
		Gly B:284 - Asn B:285	[ RasMol ]
		Gly B:295 - Pro B:296	[ RasMol ]
		Leu A:74 - Pro A:75	[ RasMol ]
		Leu B:74 - Pro B:75	[ RasMol ]
		Trp A:46 - Pro A:47	[ RasMol ]
		Trp B:46 - Pro B:47	[ RasMol ]

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	4ay8
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	2.1.1.247
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	Q8PXZ6_METMA \| Q8PXZ6	:	4ay7

4ay7	METHYLTRANSFERASE FROM METHANOSARCINA MAZEI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 31)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File