1F38 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY CRYSTALLOGRAPHIC STRUCTURE OF PRECORRIN 8W DECARBOXYLASE, THE PRODUCT OF GENE MT0146 IN THE METHANOBACTERIUM THERMOAUTOTROPHICUM GENOME

Authors :   J. P. Keller, P. M. Smith, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   31 May 00 (Deposition) - 10 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Decarboxylase, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. P. Keller, P. M. Smith, J. Benach, D. Christendat, G. T. Detitta, J. F. Hunt
The Crystal Structure Of Mt0146/Cbit Suggests That The Putative Precorrin-8W Decarboxylase Is A Methyltransferase
Structure V. 10 1475 2002
PubMed-ID: 12429089 | Reference-DOI: 10.1016/S0969-2126(02)00876-6
(for further references see the PDB file header)

Molecule 1 - PRECORRIN-8W DECARBOXYLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14A DERIVATIVE
	Expression System Taxid	:	562
	Gene	:	MT0146
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	Organism Taxid	:	145262
	Other Details	:	GENOMIC DNA

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 32)

No.	Name	Count	Type	Full Name
1	MSE	32	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1F38)

Asymmetric/Biological Unit

No.	Residues
1	A:1123	-	D:4127
2	A:1127	-	D:4123
3	B:2123	-	C:3127
4	B:2127	-	C:3123

Asymmetric/Biological Unit

No.	Residues
1	Gly A:1115	-	Pro A:1116
2	Gly B:2115	-	Pro B:2116
3	Gly C:3115	-	Pro C:3116
4	Gly D:4115	-	Pro D:4116

(no "SAP(SNP)/Variant" information available for 1F38)

(no "PROSITE Motif" information available for 1F38)

(no "Exon" information available for 1F38)

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:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
          CBIT_METTH      1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV  186
               SCOP domains d1f38a_ A: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1f38A00 A:1102-1286 Vaccinia Virus protein VP39                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhh....eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1f38 A 1101 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 1286
                            |     1110      1120     |1130      1140      1150      1160      1170  |   1180      1190      1200      1210      1220      1230      1240   |  1250      1260      1270 ||   1280      
                            |              1119-MSE  |                                           1173-MSE      1187-MSE                                                 1244-MSE                    1272-MSE          
                         1101-MSE                 1126-MSE                                                                                                                                           1273-MSE

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
          CBIT_METTH      1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV  186
               SCOP domains d1f38b_ B: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1f38B00 B:2102-2286 Vaccinia Virus protein VP39                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhh....eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1f38 B 2101 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 2286
                            |     2110      2120     |2130      2140      2150      2160      2170  |   2180      2190      2200      2210      2220      2230      2240   |  2250      2260      2270 ||   2280      
                         2101-MSE          2119-MSE  |                                           2173-MSE      2187-MSE                                                 2244-MSE                    2272-MSE          
                                                  2126-MSE                                                                                                                                           2273-MSE

Chain C from PDB  Type:PROTEIN  Length:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
          CBIT_METTH      1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV  186
               SCOP domains d1f38c_ C: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1f38C00 C:3102-3286 Vaccinia Virus protein VP39                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh...eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1f38 C 3101 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 3286
                            |     3110      3120     |3130      3140      3150      3160      3170  |   3180      3190      3200      3210      3220      3230      3240   |  3250      3260      3270 ||   3280      
                         3101-MSE          3119-MSE  |                                           3173-MSE      3187-MSE                                                 3244-MSE                    3272-MSE          
                                                  3126-MSE                                                                                                                                           3273-MSE

Chain D from PDB  Type:PROTEIN  Length:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
          CBIT_METTH      1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV  186
               SCOP domains d1f38d_ D: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1f38D00 D:4102-4286 Vaccinia Virus protein VP39                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh...eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1f38 D 4101 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 4286
                            |     4110      4120     |4130      4140      4150      4160      4170  |   4180      4190      4200      4210      4220      4230      4240   |  4250      4260      4270 ||   4280      
                         4101-MSE          4119-MSE  |                                           4173-MSE      4187-MSE                                                 4244-MSE                    4272-MSE          
                                                  4126-MSE                                                                                                                                           4273-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/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Methanothermobacter thermautotrophicus. Organism_taxid: 145262. (5)

1a	1f38A00	A:1102-1286
1b	1f38B00	B:2102-2286
1c	1f38C00	C:3102-3286
1d	1f38D00	D:4102-4286

(no "Pfam Domain" information available for 1F38)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (CBIT_METTH | O26249)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0008276	protein methyltransferase activity	Catalysis of the transfer of a methyl group (CH3-) to a protein.
	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:0009236	cobalamin biosynthetic process	The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0046140	corrin biosynthetic process	The chemical reactions and pathways resulting in the formation of corrin, C19H22N4, the fundamental heterocyclic skeleton of the corrinoids. It consists of four reduced pyrrole rings joined into a macrocyclic ring. Corrin is the core of the vitamin B12 molecule.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006479	protein methylation	The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.

Asymmetric/Biological Unit
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	Sites
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	Cis Peptide Bonds
		Gly A:1115 - Pro A:1116	[ RasMol ]
		Gly B:2115 - Pro B:2116	[ RasMol ]
		Gly C:3115 - Pro C:3116	[ RasMol ]
		Gly D:4115 - Pro D:4116	[ RasMol ]

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	1f38
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 32)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

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