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Title :   CRYSTAL STRUCTURE OF THE NATIVE FORM OF UROPORPHYRIN III C-METHYL TRANSFERASE FROM THERMUS THERMOPHILUS

Authors :   P. H. Rehse, T. Kitao, T. H. Tahirov, Riken Structural Genomics/Prot Initiative (Rsgi)

Date :   05 Feb 04 (Deposition) - 15 Feb 05 (Release) - 28 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

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

Keywords :   Transferase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. H. Rehse, T. Kitao, T. H. Tahirov
Structure Of A Closed-Form Uroporphyrinogen-Iii C-Methyltransferase From Thermus Thermophilus.
Acta Crystallogr. , Sect. D V. 61 913 2005
PubMed-ID: 15983414 | Reference-DOI: 10.1107/S0907444905008838

Molecule 1 - UROPORPHYRIN-III C-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.107
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	HYPOTHETICAL PROTEIN TTHA0667

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:86 , THR A:114 , SER A:115 , HOH A:608	BINDING SITE FOR RESIDUE CL A 501
2	AC2	SOFTWARE	GLY B:85 , ASP B:86 , THR B:114	BINDING SITE FOR RESIDUE CL B 502
3	AC3	SOFTWARE	GLY B:207	BINDING SITE FOR RESIDUE CL B 503
4	AC4	SOFTWARE	ARG A:152 , ARG A:177 , ASP A:178 , HOH A:648	BINDING SITE FOR RESIDUE EDO A 601
5	AC5	SOFTWARE	ARG B:152 , ARG B:177 , HOH B:643	BINDING SITE FOR RESIDUE EDO B 602
6	AC6	SOFTWARE	PRO A:77 , ARG B:195 , VAL B:209 , GLU B:210 , HOH B:719	BINDING SITE FOR RESIDUE EDO B 603
7	AC7	SOFTWARE	ARG A:102 , LYS B:26 , GLU B:228 , HOH B:658	BINDING SITE FOR RESIDUE EDO B 604
8	AC8	SOFTWARE	TYR A:5 , ARG A:23 , GLU A:27 , PHE A:78	BINDING SITE FOR RESIDUE EDO A 605

(no "SS Bond" information available for 1VA0)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:213	-	Pro A:214
2	Pro B:213	-	Pro B:214

(no "SAP(SNP)/Variant" information available for 1VA0)

(no "PROSITE Motif" information available for 1VA0)

(no "Exon" information available for 1VA0)

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:221
 aligned with Q5SKH6_THET8 | Q5SKH6 from UniProtKB/TrEMBL  Length:240

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
         Q5SKH6_THET8     2 GRVYLVGAGPGDPELLTLKAYRLLKEAPVVLYDRLVDERVLALAPGEKVYVGKEEGESEKQEEIHRLLLRHARAHPFVVRLKGGDPMVFGRGGEEVLFLLRHGVPVEVVPGVTSLLASGLPLTHRGLAHGFAAVSGVLEGGGYPDLRPFARVPTLVVLMGVGRRVWIAKELLRLGRDPREPTLFVERASTPKERRVHARLEEVAEGKVEVRPPALWILGEVVRVF 226
               SCOP domains d1va0a_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 1va0A01 A:2-114 Cobalt-precorrin-4 Transmethylase; Doma    in 1                                                  1va0A02 A:115-226 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh.eeee....hhhhhh....eeee.....----hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhh...eeee...hhhhh............eeeeee..hhhhh............eeee....hhhhhhhhhhhh......eeeeee.......eeeeeehhhhhh........eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1va0 A   2 GRVYLVGAGPGDPELLTLKAYRLLKEAPVVLYDRLVDERVLALAPGEKVYVGKEE----KQEEIHRLLLRHARAHPFVVRLKGGDPMVFGRGGEEVLFLLRHGVPVEVVPGVTSLLASGLPLTHRGLAHGFAAVSGVLEGGGYPDLRPFARVPTLVVLMGVGRRVWIAKELLRLGRDPREPTLFVERASTPKERRVHARLEEVAEGKVEVRPPALWILGEVVRVF 226
                                    11        21        31        41        51    |   61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                 56   61

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with Q5SKH6_THET8 | Q5SKH6 from UniProtKB/TrEMBL  Length:240

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q5SKH6_THET8     2 GRVYLVGAGPGDPELLTLKAYRLLKEAPVVLYDRLVDERVLALAPGEKVYVGKEEGESEKQEEIHRLLLRHARAHPFVVRLKGGDPMVFGRGGEEVLFLLRHGVPVEVVPGVTSLLASGLPLTHRGLAHGFAAVSGVLEGGGYPDLRPFARVPTLVVLMGVGRRVWIAKELLRLGRDPREPTLFVERASTPKERRVHARLEEVAEGKVEVRPPALWILGEVVRVFAEKEAPVDALAL 238
               SCOP domains d1va0b_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 1va0B01 B:2-114 Cobalt-precorrin-4 Transmethylase;           Domain 1                                            1va0B02 B:115-238 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                             CATH domains
           Pfam domains (1) -TP_methylase-1va0B01 B:3-205                                                                                                                                                                               --------------------------------- Pfam domains (1)
           Pfam domains (2) -TP_methylase-1va0B02 B:3-205                                                                                                                                                                               --------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh.eeee....hhhhhh....eeee.----------..hhhhhhhhhhhh.eeeeee........hhhhhhhhhhhh...eeee...hhhhh............eeeeee..................eeeee....hhhhhhhhhhhh......eeeeee.......eeeeeehhhhhh........eeeee.hhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1va0 B   2 GRVYLVGAGPGDPELLTLKAYRLLKEAPVVLYDRLVDERVLALAPGEKVYV----------EEIHRLLLRHARAHPFVVRLKGGDPMVFGRGGEEVLFLLRHGVPVEVVPGVTSLLASGLPLTHRGLAHGFAAVSGVLEGGGYPDLRPFARVPTLVVLMGVGRRVWIAKELLRLGRDPREPTLFVERASTPKERRVHARLEEVAEGKVEVRPPALWILGEVVRVFAEKEAPVDALAL 238
                                    11        21        31        41        51|        - |      71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
                                                                             52         63

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: Tetrapyrrole methylase (96)

Protein domain: automated matches (4)

Thermus thermophilus HB8 [TaxId: 300852] (2)

1a	d1va0a_	A:
1b	d1va0b_	B:

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: TP_methylase (35)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (4)

1a	TP_methylase-1va0B01	B:3-205
1b	TP_methylase-1va0B02	B:3-205

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q5SKH6_THET8 | Q5SKH6)

molecular function
	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.
biological process
	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.
	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/Biological Unit
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	Cis Peptide Bonds
		Pro A:213 - Pro A:214	[ RasMol ]
		Pro B:213 - Pro B:214	[ RasMol ]

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1v9a	S-ANDEYL HOMOCYSTEINE COMPLEXED FORM RELATED ID: TTK003000228.2 RELATED DB: TARGETDB

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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