2P9D - JenaLib

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Title :   CRYSTAL STRUCTURE OF PH0725 FROM PYROCOCCUS HORIKOSHII OT3

Authors :   H. Yamamoto, M. Taketa, Y. Morikawa, Y. Matsuura, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   25 Mar 07 (Deposition) - 25 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sugahara, N. Kunishima
Crystal Structure Of Ph0725 From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

Molecule 1 - DIPHTHINE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.1.1.98
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DPHB
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	DIPHTHAMIDE BIOSYNTHESIS METHYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:10 , THR A:36 , SER A:37 , GLY A:86 , ASP A:87 , VAL A:90 , SER A:115 , ILE A:116 , PHE A:165 , LEU A:166 , LEU A:206 , ARG A:208 , ALA A:209 , PRO A:233 , HIS A:234 , ILE A:235 , HOH A:1319 , HOH A:1372 , HOH A:1485	BINDING SITE FOR RESIDUE SAH A 1301
2	AC2	SOFTWARE	PHE B:34 , LEU B:38 , MET B:39 , THR B:42 , THR B:43 , LEU B:44	BINDING SITE FOR RESIDUE GOL B 1401
3	AC3	SOFTWARE	ARG B:46 , LYS B:129 , HIS B:243 , HOH B:1441	BINDING SITE FOR RESIDUE FMT B 501
4	AC4	SOFTWARE	TYR B:117 , HOH B:1429 , HOH B:1438 , HOH B:1445	BINDING SITE FOR RESIDUE FMT B 502

(no "SS Bond" information available for 2P9D)

Asymmetric Unit

No.	Residues
1	Pro A:232	-	Pro A:233
2	Pro B:232	-	Pro B:233

(no "SAP(SNP)/Variant" information available for 2P9D)

(no "PROSITE Motif" information available for 2P9D)

(no "Exon" information available for 2P9D)

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
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Chain A from PDB  Type:PROTEIN  Length:265
 aligned with DPHB_PYRHO | O58456 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
           DPHB_PYRHO     1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
               SCOP domains d2p9da_ A: Diphthine synthase, DphB                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2p9dA01 A:1-114 Cobalt-precorrin-4 Transmethylase; Domain 1                                                       2p9dA02 A:115-265 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhh..eeeee...hhhhhhhhhh.hhhhh...eee.........hhhhhhhhhhhhh...eeeee.eehhhhee.hhhhhhhhhhhhhhhhh........eeeeee.......eeeeeehhhhh........eeeee....hhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p9d A   1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVMSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with DPHB_PYRHO | O58456 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
           DPHB_PYRHO     1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
               SCOP domains d2p9db_ B: Diphthine synthase, DphB                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2p9dB01 B:1-114 Cobalt-precorrin-4 Transmethylase; Domain 1                                                       2p9dB02 B:115-265 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                                        CATH domains
           Pfam domains (1) -TP_methylase-2p9dB01 B:2-225                                                                                                                                                                                                    ---------------------------------------- Pfam domains (1)
           Pfam domains (2) -TP_methylase-2p9dB02 B:2-225                                                                                                                                                                                                    ---------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhh..eeeee...hhhhhhhhhh.hhhhh...eee.........hhhhhhhhhhhhh...eeeee.ee....ee.hhhhhhhhhhhhhhhhh........eeeeee.......eeeeeehhhhh........eeeee....hhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p9d B   1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVMSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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: Tetrapyrrole methylase (104)

Superfamily: Tetrapyrrole methylase (104)

Family: Tetrapyrrole methylase (96)

Protein domain: Diphthine synthase, DphB (82)

Pyrococcus horikoshii [TaxId: 53953] (80)

1a	d2p9da_	A:
1b	d2p9db_	B:

Asymmetric Unit(hide GO term definitions)

Chain A,B (DPHB_PYRHO | O58456)

molecular function
	GO:0004164	diphthine synthase activity	Catalysis of the reaction: S-adenosyl-L-methionine + 2-(3-carboxy-3-aminopropyl)-L-histidine = S-adenosyl-L-homocysteine + 2-(3-carboxy-3-(methylammonio)propyl)-L-histidine.
	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:0050843	S-adenosylmethionine catabolic process	The chemical reactions and pathways resulting in the breakdown of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	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:0017183	peptidyl-diphthamide biosynthetic process from peptidyl-histidine	The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.

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		Pro B:232 - Pro B:233	[ RasMol ]

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Description

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