4AY7 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   METHYLTRANSFERASE FROM METHANOSARCINA MAZEI

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

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

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Transferase, Tim Barrel (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
	Expression System Vector	:	PET-15B
	Expression System Vector Type	:	PLASMID
	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 (3, 6)

No.	Name	Count	Type	Full Name
1	CSD	2	Mod. Amino Acid	3-SULFINOALANINE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:240 , CYS A:242 , CYS A:319	BINDING SITE FOR RESIDUE ZN A 500
2	AC2	SOFTWARE	GLU A:88 , LYS A:273 , ASP A:313 , HOH A:2067 , HOH A:2068 , HOH A:2199 , HOH A:2201	BINDING SITE FOR RESIDUE MG A 600
3	AC3	SOFTWARE	HIS B:240 , CYS B:242 , GLU B:263 , CYS B:319	BINDING SITE FOR RESIDUE ZN B 500
4	AC4	SOFTWARE	GLU B:88 , ASP B:313 , HOH B:2065 , HOH B:2182 , HOH B:2184 , HOH B:2185	BINDING SITE FOR RESIDUE MG B 600

(no "SS Bond" information available for 4AY7)

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 4AY7)

(no "PROSITE Motif" information available for 4AY7)

(no "Exon" information available for 4AY7)

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:337
 aligned with Q8PXZ6_METMA | Q8PXZ6 from UniProtKB/TrEMBL  Length:342

    Alignment length:337
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       
         Q8PXZ6_METMA     6 EFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELMDVVGAPWPEAHTNPELMAKLALANHELSGLEAVRLPYCLTVLVEAMGCEINMGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGMEGPVTVASDLVSVKSFMKWSIKKTDLLEQALDIATEASIIYANAMVEAGADVIAIADPVASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPMTPLENVKALVAARDEFYA 342
               SCOP domains d4ay7a_ 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
                 4ay7 A   6 EFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELMDVVGAPWPEAHTNPELMAKLALANHELSGLEAVRLPYcLTVLVEAMGCEINMGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGMEGPVTVASDLVSVKSFMKWSIKKTDLLEQALDIATEASIIYANAMVEAGADVIAIADPVASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPMTPLENVKALVAARDEFYA 342
                                    15        25        35        45        55        65        75 |      85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       
                                                                                                  77-CSD

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with Q8PXZ6_METMA | Q8PXZ6 from UniProtKB/TrEMBL  Length:342

    Alignment length:337
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       
         Q8PXZ6_METMA     6 EFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELMDVVGAPWPEAHTNPELMAKLALANHELSGLEAVRLPYCLTVLVEAMGCEINMGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGMEGPVTVASDLVSVKSFMKWSIKKTDLLEQALDIATEASIIYANAMVEAGADVIAIADPVASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPMTPLENVKALVAARDEFYA 342
               SCOP domains d4ay7b_ 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........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ay7 B   6 EFTLKTRLLAALKGEPVDKVPVCSVTQTGIVELMDVVGAPWPEAHTNPELMAKLALANHELSGLEAVRLPYcLTVLVEAMGCEINMGTKNRQPSVTGHPYPKDLEGAAVPADLLQRGRIPVVLEAIKIIREKVGPDVPIVGGMEGPVTVASDLVSVKSFMKWSIKKTDLLEQALDIATEASIIYANAMVEAGADVIAIADPVASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKIGSAKKGKEVIGTRARLVGNVSSPFTLLPGPVDKIKAEAKEALEGGIDVLAPGCGIAPMTPLENVKALVAARDEFYA 342
                                    15        25        35        45        55        65        75 |      85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       
                                                                                                  77-CSD

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	d4ay7a_	A:
1b	d4ay7b_	B:

(no "CATH Domain" information available for 4AY7)

(no "Pfam Domain" information available for 4AY7)

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.

Asymmetric Unit
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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 ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	2.1.1.247
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UniProtKB/TrEMBL
	Q8PXZ6_METMA \| Q8PXZ6	:	4ay8

4ay8	SEMET-DERIVATIVE OF A METHYLTRANSFERASE FROM M. MAZEI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

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

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SCOP Domains (1, 2)

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Gene Ontology (7, 7)

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Related Entries

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