1PJT - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   THE STRUCTURE OF THE SER128ALA POINT-MUTANT VARIANT OF CYSG, THE MULTIFUNCTIONAL METHYLTRANSFERASE/DEHYDROGENASE/FERROCHELATASE FOR SIROHEME SYNTHESIS

Authors :   M. E. Stroupe, H. K. Leech, D. S. Daniels, M. J. Warren, E. D. Getzoff

Date :   03 Jun 03 (Deposition) - 02 Dec 03 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Rossmann Fold, Nucleotide Binding Motif, Sah, Sam, Nad, Phosphoserine, Transferase-Oxidoreductase-Lyase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Stroupe, H. K. Leech, D. S. Daniels, M. J. Warren, E. D. Getzoff
Cysg Structure Reveals Tetrapyrrole-Binding Features And Novel Regulation Of Siroheme Biosynthesis.
Nat. Struct. Biol. V. 10 1064 2003
PubMed-ID: 14595395 | Reference-DOI: 10.1038/NSB1007

Molecule 1 - SIROHEME SYNTHASE
	Chains	:	A, B
	EC Number	:	2.1.1.107, 1.-.-.-, 4.99.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	S128A-PBAD-HIS-MYC
	Expression System Strain	:	LMG194
	Expression System Taxid	:	562
	Expression System Vector Type	:	PBR522
	Gene	:	CYSG OR STM3477
	Mutation	:	YES
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Other Details	:	RESIDUES 1-212 (CYSGB) ARE A DEHYDROGENASE/FERROCHELATASE, RESIDUES 213-457 (CYSGA) ARE A BISMETHYLTRANSFERASE
	Synonym	:	CYSG

		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	PO4	1	Ligand/Ion	PHOSPHATE ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:261 , ASP A:262 , HOH A:522 , SER B:115 , ARG B:137 , ARG B:140 , HOH B:535 , HOH B:552	BINDING SITE FOR RESIDUE PO4 B 503
2	AC2	SOFTWARE	PRO A:225 , GLY A:301 , GLY A:302 , ASP A:303 , ILE A:306 , PHE A:307 , THR A:331 , ALA A:332 , TYR A:381 , MET A:382 , VAL A:408 , GLY A:411 , PRO A:436 , ALA A:437 , HOH A:543 , HOH A:581	BINDING SITE FOR RESIDUE SAH A 501
3	AC3	SOFTWARE	PRO B:225 , LEU B:250 , GLY B:301 , GLY B:302 , ASP B:303 , ILE B:306 , PHE B:307 , THR B:331 , ALA B:332 , CYS B:336 , TYR B:381 , MET B:382 , VAL B:408 , ASN B:410 , GLY B:411 , PRO B:436 , ALA B:437 , LEU B:438 , HOH B:538 , HOH B:539	BINDING SITE FOR RESIDUE SAH B 502

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

Asymmetric/Biological Unit

No.	Residues
1	Ser A:120	-	Pro A:121
2	Ser A:435	-	Pro A:436
3	Ser B:120	-	Pro B:121
4	Ser B:435	-	Pro B:436

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

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.	CYSG_SALTY	221-235	2	A:221-235 B:221-235
2	SUMT_2	PS00840	Uroporphyrin-III C-methyltransferase signature 2.	CYSG_SALTY	296-329	2	A:296-329 B:296-329

(no "Exon" information available for 1PJT)

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:448
 aligned with CYSG_SALTY | P25924 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:457
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
           CYSG_SALTY     1 MDHLPIFCQLRDRDCLIVGGGDVAERKARLLLEAGARLTVNALTFIPQFTVWANEGMLTLVEGPFDETLLDSCWLAIAATDDDTVNQRVSDAAESRRIFCNVVDAPKAASFIMPSIIDRSPLMVAVSSGGTSPVLARLLREKLESLLPQHLGQVARYAGQLRARVKKQFATMGERRRFWEKFFVNDRLAQSLANADEKAVNATTERLFSEPLDHRGEVVLVGAGPGDAGLLTLKGLQQIQQADIVVYDRLVSDDIMNLVRRDADRVFVGKRAGYHCVPQEEINQILLREAQKGKRVVRLKGGDPFIFGRGGEELETLCHAGIPFSVVPGITAASGCSAYSGIPLTHRDYAQSVRLVTGHLKTGGELDWENLAAEKQTLVFYMGLNQAATIQEKLIAFGMQADMPVALVENGTSVKQRVVHGVLTQLGELAQQVESPALIIVGRVVALRDKLNWFSNH 457
               SCOP domains d1pjta1 A:1-113 Siroheme synthase CysG, domain 1                                                                 d1pjta3 A:114-215 Siroheme synthase CysG, domains 2 and 3                                             d1pjta2 A:216-457 Siroheme synthase CysG, domains 4 and    5                                                                                                                                                                                       SCOP domains
               CATH domains 1pjtA01 A:1-112 NAD(P)-binding Rossmann-like Domain                                                             1pjtA02 A:113-148                   1pjtA03 A:149-213                                                1pjtA04 A:214-331 Cobalt-precorrin-4 Transmethylase; Domai   n 1                                                      1pjtA05 A:332-457 Methyltr      ansferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee..hhhhhhhhhhhhh...eeeeee...hhhhhhhhh....eeee...hhhhhh...eeee...hhhhhhhhhhhhhhh..eeee........ee..eeeee..eeeeee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhh..eeee....hhhhhh......eeee....---...hhhhhhhhhhhhhhh..eeeeee........hhhhhhh........eeee...hhhhhhhhhh...........eeeee.------...hhhhhhh...eeee.....hhhhhhhhhhhh......eeeeee.......eeeeee..hhhhhhhhh...eeeee.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUMT_1         ------------------------------------------------------------SUMT_2  PDB: A:296-329            -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pjt A   1 MDHLPIFCQLRDRDCLIVGGGDVAERKARLLLEAGARLTVNALTFIPQFTVWANEGMLTLVEGPFDETLLDSCWLAIAATDDDTVNQRVSDAAESRRIFCNVVDAPKAASFIMPSIIDRSPLMVAVSAGGTSPVLARLLREKLESLLPQHLGQVARYAGQLRARVKKQFATMGERRRFWEKFFVNDRLAQSLANADEKAVNATTERLFSEPLDHRGEVVLVGAGPGDAGLLTLKGLQQIQQADIVVYDRLVSDDIMNLVRRDADRVFVGKR---HCVPQEEINQILLREAQKGKRVVRLKGGDPFIFGRGGEELETLCHAGIPFSVVPGITAASGCSAYSGIPLTHRDYAQSVRLVT------GELDWENLAAEKQTLVFYMGLNQAATIQEKLIAFGMQADMPVALVENGTSVKQRVVHGVLTQLGELAQQVESPALIIVGRVVALRDKLNWFSNH 457
                                    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       270|   |  280       290       300       310       320       330       340       350      |  -   |   370       380       390       400       410       420       430       440       450       
                                                                                                                                                                                                                                                                                                        271 275                                                                               357    364

Chain B from PDB  Type:PROTEIN  Length:455
 aligned with CYSG_SALTY | P25924 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:457
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
           CYSG_SALTY     1 MDHLPIFCQLRDRDCLIVGGGDVAERKARLLLEAGARLTVNALTFIPQFTVWANEGMLTLVEGPFDETLLDSCWLAIAATDDDTVNQRVSDAAESRRIFCNVVDAPKAASFIMPSIIDRSPLMVAVSSGGTSPVLARLLREKLESLLPQHLGQVARYAGQLRARVKKQFATMGERRRFWEKFFVNDRLAQSLANADEKAVNATTERLFSEPLDHRGEVVLVGAGPGDAGLLTLKGLQQIQQADIVVYDRLVSDDIMNLVRRDADRVFVGKRAGYHCVPQEEINQILLREAQKGKRVVRLKGGDPFIFGRGGEELETLCHAGIPFSVVPGITAASGCSAYSGIPLTHRDYAQSVRLVTGHLKTGGELDWENLAAEKQTLVFYMGLNQAATIQEKLIAFGMQADMPVALVENGTSVKQRVVHGVLTQLGELAQQVESPALIIVGRVVALRDKLNWFSNH 457
               SCOP domains d1pjtb1 B:1-113 Siroheme synthase CysG, domain 1                                                                 d1pjtb3 B:114-215 Siroheme synthase CysG, domains 2 and 3                                             d1pjtb2 B:216-457 Siroheme synthase CysG, domains 4 and 5                                                                                                                                                                                          SCOP domains
               CATH domains 1pjtB01 B:1-112 NAD(P)-binding Rossmann-like Domain                                                             1pjtB02 B:113-148                   1pjtB03 B:149-214                                                 1pjtB04 B:215-331 Cobalt-precorrin-4 Transmethylase; Domai  n 1                                                      1pjtB05 B:332-457 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                               CATH domains
           Pfam domains (1) -----NAD_binding_7-1pjtB01 B:6-115                                                                                 ---------------------------------CysG_dimeriser-1pjtB03 B:149-209                             -------TP_methylase-1pjtB05 B:217-427                                                                                                                                                                                     ------------------------------ Pfam domains (1)
           Pfam domains (2) -----NAD_binding_7-1pjtB02 B:6-115                                                                                 ---------------------------------CysG_dimeriser-1pjtB04 B:149-209                             -------TP_methylase-1pjtB06 B:217-427                                                                                                                                                                                     ------------------------------ Pfam domains (2)
         Sec.struct. author ...eeeee.....eeeee..hhhhhhhhhhhhhh..eeeeee...hhhhhhhhh....eeee...hhhhhh...eeee...hhhhhhhhhhhhhhh..eeee........ee..eeeee..eeeeee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhh...eeee....hhhhhh......eeee.....--...hhhhhhhhhhhhhhh..eeeeee..........hhhhhh.......eeee...hhhhhhhhh............eeeeee.........hhhhhh....eeeee.hhhhhhhhhhhhhh.......eeeeee.......eeeeee..hhhhhhh.....eeeee.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUMT_1         ------------------------------------------------------------SUMT_2  PDB: B:296-329            -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pjt B   1 MDHLPIFCQLRDRDCLIVGGGDVAERKARLLLEAGARLTVNALTFIPQFTVWANEGMLTLVEGPFDETLLDSCWLAIAATDDDTVNQRVSDAAESRRIFCNVVDAPKAASFIMPSIIDRSPLMVAVSAGGTSPVLARLLREKLESLLPQHLGQVARYAGQLRARVKKQFATMGERRRFWEKFFVNDRLAQSLANADEKAVNATTERLFSEPLDHRGEVVLVGAGPGDAGLLTLKGLQQIQQADIVVYDRLVSDDIMNLVRRDADRVFVGKRA--HCVPQEEINQILLREAQKGKRVVRLKGGDPFIFGRGGEELETLCHAGIPFSVVPGITAASGCSAYSGIPLTHRDYAQSVRLVTGHLKTGGELDWENLAAEKQTLVFYMGLNQAATIQEKLIAFGMQADMPVALVENGTSVKQRVVHGVLTQLGELAQQVESPALIIVGRVVALRDKLNWFSNH 457
                                    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       270 |  |  280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
                                                                                                                                                                                                                                                                                                         272  |                                                                                                                                                                                      
                                                                                                                                                                                                                                                                                                            275

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(hide GO term definitions)

Chain A,B (CYSG_SALTY | P25924)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004325	ferrochelatase activity	Catalysis of the reaction: protoheme = Fe(2+) + protoporphyrin IX.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0043115	precorrin-2 dehydrogenase activity	Catalysis of the reaction: NAD(+) + precorrin-2 = 2 H(+) + NADH + sirohydrochlorin.
	GO:0051266	sirohydrochlorin ferrochelatase activity	Catalysis of the reaction: siroheme + 2 H+ = Fe(2+) + sirohydrochlorin.
	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:0004851	uroporphyrin-III C-methyltransferase activity	Catalysis of the reaction: 2 S-adenosyl-L-methionine + uroporphyrin III = 2 S-adenosyl-L-homocysteine + precorrin-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.
	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.
	GO:0019354	siroheme biosynthetic process	The chemical reactions and pathways resulting in the formation of siroheme, a tetrahydroporphyrin with adjacent, reduced pyrrole rings.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:120 - Pro A:121	[ RasMol ]
		Ser A:435 - Pro A:436	[ RasMol ]
		Ser B:120 - Pro B:121	[ RasMol ]
		Ser B:435 - Pro B:436	[ RasMol ]

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	1pjt
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	CYSG_SALTY \| P25924
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	1.-.-.-
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	2.1.1.107
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	4.99.1.-
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UniProtKB/Swiss-Prot
	CYSG_SALTY \| P25924	:	1pjq 1pjs

1pjq	NATIVE CYSG
1pjs	NAD-COCRYSTAL STRUCTURE OF CYSG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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