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Title :   TIME-RESOLVED AND STATIC-ENSEMBLE STRUCTURAL CHEMISTRY OF HYDROXYMETHYLBILANE SYNTHASE

Authors :   J. R. Helliwell, Y. P. Nieh, J. Habash, P. F. Faulder, J. Raftery, M. Wulf A. Hadener

Date :   16 Jan 02 (Deposition) - 16 Jan 03 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase, Biosynthesis Of Linear Tetrapyrrole, All Alpha/Beta (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Helliwell, Y. P. Nieh, J. Habash, P. F. Faulder, J. Raftery, M. Cianci, M. Wulff, A. Hadener
Time-Resolved And Static-Ensemble Structural Chemistry Of Hydroxymethylbilane Synthase
Faraday Discuss. V. 122 131 2003
PubMed-ID: 12555854 | Reference-DOI: 10.1039/B201331B
(for further references see the PDB file header)

Molecule 1 - PORPHOBILINOGEN DEAMINASE
	Chains	:	A
	EC Number	:	2.5.1.61
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	THREE DOMAINS
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO CYSTEINE 242
	Synonym	:	HYDROXYMETHYLBILANE SYNTHASE, PBG, HMBS, HYDROXYMETHYLBILANE SYNTHASE, PRE-UROPORPHYRINOGEN SYNTHASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	DPM	1	Ligand/Ion	3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:15 , SER A:81 , LYS A:83 , ASP A:84 , THR A:127 , SER A:128 , SER A:129 , ARG A:131 , ARG A:132 , LEU A:148 , ARG A:155 , LEU A:169 , ALA A:170 , GLN A:198 , GLY A:199 , CYS A:242 , HOH A:2197 , HOH A:2317 , HOH A:2318 , HOH A:2319 , HOH A:2320	BINDING SITE FOR RESIDUE DPM A 315

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

(no "Cis Peptide Bond" information available for 1GTK)

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PORPHOBILINOGEN_DEAM	PS00533	Porphobilinogen deaminase cofactor-binding site.	HEM3_ECOLI	231-247	1	A:231-247

(no "Exon" information available for 1GTK)

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:294
 aligned with HEM3_ECOLI | P06983 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
           HEM3_ECOLI     3 DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEVYNGDAPA 313
               SCOP domains d1gtka1 A:3-219 Porphobilinogen deaminas                 e (hydroxymethylbilane synthase), N-terminal domain                                                                                                             d1gtka2 A:220-313 Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain  SCOP domains
               CATH domains 1gtkA01 A:3-99,A:200-220 Periplasmic bin                 ding protein-like II                    1gtkA02 A:100-199 Periplasmic binding protein-like II                                               1gtkA01              1gtkA03 A:221-306  [code=3.30.160.40, no name defined]                                ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee..-----------------..hhhhhhhhhhh....eeeee.hhh.......eeeeee.......eeee.....hhhhh....eee..hhhhhhhhhhhh...eee....hhhhhhhhhhh....eeeeehhhhhhh.hhhhh.ee..............eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeeee......eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PORPHOBILINOGEN_D------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gtk A   3 DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMV-----------------GLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEVYNGDAPA 313
                                    12        22        32        42         -       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
                                                                  42                60

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: [code=3.30.160.40, no name defined] (5)

Escherichia coli. Organism_taxid: 562. (4)

1gtkA03

A:221-306

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

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Escherichia coli. Organism_taxid: 562. (17)

2a	1gtkA01	A:3-99,A:200-220
2b	1gtkA02	A:100-199

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HEM3_ECOLI | P06983)

molecular function
	GO:0004418	hydroxymethylbilane synthase activity	Catalysis of the reaction: H(2)O + 4 porphobilinogen = hydroxymethylbilane + 4 NH(4)(+).
	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:0006783	heme biosynthetic process	The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
	GO:0018160	peptidyl-pyrromethane cofactor linkage	The covalent binding of a pyrromethane (dipyrrin) cofactor to protein via the sulfur atom of cysteine forming dipyrrolylmethanemethyl-L-cysteine.
	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:0006782	protoporphyrinogen IX biosynthetic process	The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
	GO:0033014	tetrapyrrole biosynthetic process	The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	2.5.1.61
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UniProtKB/Swiss-Prot
	HEM3_ECOLI \| P06983	:	1ah5 1pda 1ypn 2ypn

1ah5	REDUCED FORM SELENOMETHIONINE-LABELLED HYDROXYMETHYLBILANE SYNTHASE DETERMINED BY MAD
1ypn	REDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL STRUCTURE AFTER 2 HOURS IN A FLOW CELL DETERMINED BY TIME-RESOLVED LAUE DIFFRACTION
2ypn	REDUCED FORM HYDROXYLMETHYLBILANE SYNTHASE CRYSTAL STRUCTURE

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (2, 2)

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Gene Ontology (9, 9)

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