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Title :   CRYSTAL STRUCTURE OF PRECORRIN-4 C11-METHYLTRANSFERASE FROM RHODOBACTER CAPSULATUS (NO SAH BOUND)

Authors :   A. Seyedarabi, R. W. Pickersgill

Date :   08 Jun 10 (Deposition) - 15 Jun 11 (Release) - 15 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   A. Seyedarabi, R. W. Pickersgill
Crystal Structure Of Precorrin-4 C11-Methyltransferase From Rhodobacter Capsulatus (No Sah Bound)
To Be Published
PubMed: search

Molecule 1 - PRECORRIN-4 C(11)-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.133
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	COBM
	Organism Common	:	RHODOPSEUDOMONAS CAPSULATA
	Organism Scientific	:	RHODOBACTER CAPSULATUS
	Organism Taxid	:	272942
	Strain	:	SB1003
	Synonym	:	PRECORRIN-3 METHYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:82 , ASP A:83 , ILE A:86 , TRP A:87 , PRO A:111 , SER A:112 , HOH A:296 , HOH A:298 , HOH A:306	BINDING SITE FOR RESIDUE SO4 A 300
2	AC2	SOFTWARE	GLY B:82 , ASP B:83 , ILE B:86 , TRP B:87 , PRO B:111 , SER B:112 , HOH B:294	BINDING SITE FOR RESIDUE SO4 B 300
3	AC3	SOFTWARE	VAL B:129 , ALA B:130 , GLY B:158 , ALA B:159 , VAL B:160 , GLY B:225 , ARG B:226 , SER B:227	BINDING SITE FOR RESIDUE GOL B 500

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

(no "Cis Peptide Bond" information available for 3NEI)

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUMT_1	PS00839	Uroporphyrin-III C-methyltransferase signature 1.	COBM_RHOCB	6-20	2	A:6-20 B:6-20
2	SUMT_2	PS00840	Uroporphyrin-III C-methyltransferase signature 2.	COBM_RHOCB	76-109	2	A:76-109 B:76-109

(no "Exon" information available for 3NEI)

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:225
 aligned with COBM_RHOCB | O68100 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           COBM_RHOCB     1 MTVHFIGAGPGAADLITIRGRDLIASCPVCLYAGSLVPEALLAHCPPGAKIVNTAPMSLDAIIDTIAEAHAAGQDVARLHSGDLSIWSAMGEQLRRLRALNIPYDVTPGVPSFAAAAATLGAELTLPGVAQSVILTRTSGRASAMPAGETLENFARTGAVLAIHLSVHVLDEVVQKLVPHYGEDCPVAIVWRASWPDQRVVRATLATLQTSLGAELERTALILVGRSLAT 230
               SCOP domains d3neia_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhh....eeee...hhhhhhhhhhh...........eeeee.-----......hhhhhhh...eeeeeee..hhhhhhhhhhhhhh...eeeeee.......eeeeee..............eeeeee.hhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SUMT_1         -------------------------------------------------------SUMT_2  PDB: A:76-109             ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nei A   1 MTVHFIGAGPGAADLITIRGRDLIASCPVCLYAGSLVPEALLAHCPPGAKIVNTAPMSLDAIIDTIAEAHAAGQDVARLHSGDLSIWSAMGEQLRRLRALNIPYDVTPGVPSFAAAAATLGAELTLPGVAQSVILTRT-----AMPAGETLENFARTGAVLAIHLSVHVLDEVVQKLVPHYGEDCPVAIVWRASWPDQRVVRATLATLQTSLGAELERTALILVGRSLAT 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       | -   |   150       160       170       180       190       200       210       220       230
                                                                                                                                                                   138   144

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with COBM_RHOCB | O68100 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           COBM_RHOCB     1 MTVHFIGAGPGAADLITIRGRDLIASCPVCLYAGSLVPEALLAHCPPGAKIVNTAPMSLDAIIDTIAEAHAAGQDVARLHSGDLSIWSAMGEQLRRLRALNIPYDVTPGVPSFAAAAATLGAELTLPGVAQSVILTRTSGRASAMPAGETLENFARTGAVLAIHLSVHVLDEVVQKLVPHYGEDCPVAIVWRASWPDQRVVRATLATLQTSLGAELERTALILVGRSLAT 230
               SCOP domains d3neib_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -TP_methylase-3neiB01 B:2-209                                                                                                                                                                                    --------------------- Pfam domains (1)
           Pfam domains (2) -TP_methylase-3neiB02 B:2-209                                                                                                                                                                                    --------------------- Pfam domains (2)
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhh.eeee.....hhhhhh......eeee....hhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh...eeee...hhhhhhhhhhh...........eeeee.------.....hhhhhhh...eeeeeee..hhhhhhhhhhhhhh...eeeeee.......eeeeee..hhhhhh......eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SUMT_1         -------------------------------------------------------SUMT_2  PDB: B:76-109             ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nei B   1 MTVHFIGAGPGAADLITIRGRDLIASCPVCLYAGSLVPEALLAHCPPGAKIVNTAPMSLDAIIDTIAEAHAAGQDVARLHSGDLSIWSAMGEQLRRLRALNIPYDVTPGVPSFAAAAATLGAELTLPGVAQSVILTRT------MPAGETLENFARTGAVLAIHLSVHVLDEVVQKLVPHYGEDCPVAIVWRASWPDQRVVRATLATLQTSLGAELERTALILVGRSLAT 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       | -    |  150       160       170       180       190       200       210       220       230
                                                                                                                                                                   138    145

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Tetrapyrrole methylase (104)

Superfamily: Tetrapyrrole methylase (104)

Family: automated matches (8)

Protein domain: automated matches (8)

Rhodobacter capsulatus [TaxId: 272942] (2)

1a	d3neia_	A:
1b	d3neib_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: TP_methylase] (35)

Family: TP_methylase (35)

Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (2)

1a	TP_methylase-3neiB01	B:2-209
1b	TP_methylase-3neiB02	B:2-209

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (COBM_RHOCB | O68100)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0046026	precorrin-4 C11-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-4 = S-adenosyl-L-homocysteine + precorrin 5.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric/Biological Unit
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3ndc	CRYSTAL STRUCTURE OF PRECORRIN-4 C11-METHYLTRANSFERASE FROM RHODOBACTER CAPSULATUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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