1L8X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FERROCHELATASE FROM THE YEAST, SACCHAROMYCES CEREVISIAE, WITH COBALT(II) AS THE SUBSTRATE ION

Authors :   T. Karlberg, D. Lecerof, M. Gora, G. Silvegren, R. Labbe-Bois, M. Hansson, S. Al-Karadaghi

Date :   22 Mar 02 (Deposition) - 20 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Ferrochelatase, Heme Biosynthesis, Protoheme, Ferro-Lyase, Porphyrin Metallation, Cobalt, Mitochondrial Inner Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Karlberg, D. Lecerof, M. Gora, G. Silvegren, R. Labbe-Bois, M. Hansson, S. Al-Karadaghi
Metal Binding To Saccharomyces Cerevisiae Ferrochelatase
Biochemistry V. 41 13499 2002
PubMed-ID: 12427010 | Reference-DOI: 10.1021/BI0260785
(for further references see the PDB file header)

Molecule 1 - FERROCHELATASE
	Chains	:	A, B
	EC Number	:	4.99.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HEMZ
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PROTOHEME FERRO-LYASE, HEME SYNTHETASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:235	BINDING SITE FOR RESIDUE CO A 501
2	AC2	SOFTWARE	HIS B:235 , GLU B:314	BINDING SITE FOR RESIDUE CO B 502

(no "SS Bond" information available for 1L8X)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:139	-	Pro A:140

(no "SAP(SNP)/Variant" information available for 1L8X)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERROCHELATASE	PS00534	Ferrochelatase signature.	HEMH_YEAST	230-250	2	A:230-250 B:230-250

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOR176W	1	YOR176W.1	XV:662402-663583	1182	HEMH_YEAST	1-393	393	2	A:37-391 B:38-391	355 354

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:355
 aligned with HEMH_YEAST | P16622 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:355
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386     
           HEMH_YEAST    37 SPTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
               SCOP domains d1l8xa_ A: Ferrochelatase                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1l8xA01 A:37-199,A:339-391  [code=3.40.50.1400, no name defined]                                                                                                   1l8xA02 A:200-338  [code=3.40.50.1400, no name defined]                                                                                    1l8xA01 A:37-199,A:339-391                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh.....hhhhheeeeeee..hhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhh.....eeee.......hhhhhh...........hhh.eee......hhhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:37-391 UniProt: 1-393 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                 Transcript 1
                 1l8x A  37 SPTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with HEMH_YEAST | P16622 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:354
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387    
           HEMH_YEAST    38 PTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
               SCOP domains d1l8xb_ B: Ferrochelatase                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1l8xB01 B:38-199,B:339-391  [code=3.40.50.1400, no name defined]                                                                                                  1l8xB02 B:200-338  [code=3.40.50.1400, no name defined]                                                                                    1l8xB01 B:38-199,B:339-391                            CATH domains
           Pfam domains (1) Ferrochelatase-1l8xB01 B:38-357                                                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (1)
           Pfam domains (2) Ferrochelatase-1l8xB02 B:38-357                                                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhh..eeee............................eee......hhhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:38-391 UniProt: 1-393 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                Transcript 1
                 1l8x B  38 PTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387

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: Chelatase-like (149)

Superfamily: Chelatase (46)

Family: Ferrochelatase (37)

Protein domain: Ferrochelatase (34)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1l8xa_	A:
1b	d1l8xb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1400, no name defined] (36)

Baker's yeast (Saccharomyces cerevisiae) (2)

1a	1l8xA02	A:200-338
1b	1l8xB02	B:200-338
1c	1l8xB01	B:38-199,B:339-391
1d	1l8xA01	A:37-199,A:339-391

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Chelatase (20)

Family: Ferrochelatase (12)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (2)

1a	Ferrochelatase-1l8xB01	B:38-357
1b	Ferrochelatase-1l8xB02	B:38-357

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HEMH_YEAST | P16622)

molecular function
	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.
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: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.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:139 - Pro A:140	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1l8x
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HEMH_YEAST \| P16622
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.99.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HEMH_YEAST \| P16622
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HEMH_YEAST \| P16622	:	1lbq

(no "Related Entries Specified in the PDB File" available for 1L8X)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 4)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File