3G5F - JenaLib

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Title :   CRYSTALLOGRAPHIC ANALYSIS OF CYTOCHROME P450 CYP121

Authors :   P. Belin, M. H. Le Du, M. Gondry

Date :   05 Feb 09 (Deposition) - 21 Apr 09 (Release) - 09 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (2x)

Keywords :   Cytochrome, Tuberculosis, Cyp121, P450, Heme, Iron, Metal-Binding, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Belin, M. H. Le Du, A. Fielding, O. Lequin, M. Jacquet, J. B. Charbonnier, A. Lecoq, R. Thai, M. Courcon, C. Masson, C. Dugave, R. Genet, J. L. Pernodet, M. Gondry
Identification And Structural Basis Of The Reaction Catalyzed By Cyp121, An Essential Cytochrome P450 In Mycobacterium Tuberculosis.
Proc. Natl. Acad. Sci. Usa V. 106 7426 2009
PubMed-ID: 19416919 | Reference-DOI: 10.1073/PNAS.0812191106

Molecule 1 - CYTOCHROME P450 121
	Chains	:	A
	EC Number	:	1.14.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	P450 MT2

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 10)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:58 , SER A:61 , MET A:62 , LYS A:63 , HIS A:343 , HOH A:611 , HOH A:616 , HOH A:710 , HOH A:1073 , HOH A:1118	BINDING SITE FOR RESIDUE SO4 A 397
2	AC2	SOFTWARE	SER A:12 , ARG A:17 , HOH A:406 , HOH A:947 , HOH A:988 , HOH A:1047	BINDING SITE FOR RESIDUE SO4 A 398
3	AC3	SOFTWARE	VAL A:5 , LEU A:6 , LEU A:7 , ARG A:32 , ARG A:300 , HOH A:767	BINDING SITE FOR RESIDUE SO4 A 399
4	AC4	SOFTWARE	ARG A:134 , PHE A:161 , ARG A:381 , ARG A:391 , HOH A:756 , HOH A:837 , HOH A:1116	BINDING SITE FOR RESIDUE SO4 A 400
5	AC5	SOFTWARE	MET A:62 , MET A:86 , HIS A:146 , PHE A:230 , GLY A:234 , SER A:237 , PHE A:280 , LEU A:284 , ARG A:286 , ALA A:337 , PHE A:338 , GLY A:339 , HIS A:343 , CYS A:345 , PRO A:346 , HOH A:617 , HOH A:624 , HOH A:775 , HOH A:798 , HOH A:841 , HOH A:888 , HOH A:1000	BINDING SITE FOR RESIDUE HEM A 462

(no "SS Bond" information available for 3G5F)

Asymmetric Unit

No.	Residues
1	Val A:9	-	Pro A:10
2	Ala A:129	-	Pro A:130

(no "SAP(SNP)/Variant" information available for 3G5F)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTO	338-347	1	A:338-347
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTU	338-347	1	A:338-347

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTO	338-347	1	A:338-347
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTU	338-347	1	A:338-347

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTO	338-347	2	A:338-347
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTU	338-347	2	A:338-347

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTO	338-347	2	A:338-347
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP121_MYCTU	338-347	2	A:338-347

(no "Exon" information available for 3G5F)

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
	(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:394
 aligned with CP121_MYCTO | P9WPP6 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:394
                                    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       322       332       342       352       362       372       382       392    
          CP121_MYCTO     3 ATVLLEVPFSARGDRIPDAVAELRTREPIRKVRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAPRLNALTVPPEVVNNMGNIADAGLRKAVMKAITPKAPGLEQFLRDTANSLLDNLITEGAPADLRNDFADPLATALHCKVLGIPQEDGPKLFRSLSIAFMSSADPIPAAKINWDRDIEYMAGILENPNITTGLMGELSRLRKDPAYSHVSDELFATIGVTFFGAGVISTGSFLTTALISLIQRPQLRNLLHEKPELIPAGVEELLRINLSFADGLPRLATADIQVGDVLVRKGELVLVLLEGANFDPEHFPNPGSIELDRPNPTSHLAFGRGQHFCPGSALGRRHAQIGIEALLKKMPGVDLAVPIDQLVWRTRFQRRIPERLPVLW 396
               SCOP domains d3g5fa_ A: Cyp121 monooxygenase (P450 Mt2)                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3g5fA00 A:3-396 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhh...eehhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeee...eee..eee....eeeehhhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5f A   3 ATVLLEVPFSARGDRIPDAVAELRTREPIRKVRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAPRLNALTVPPEVVNNMGNIADAGLRKAVMKAITPKAPGLEQFLRDTANSLLDNLITEGAPADLRNDFADPLATALHCKVLGIPQEDGPKLFRSLSIAFMSSADPIPAAKINWDRDIEYMAGILENPNITTGLMGELSRLRKDPAYSHVSDELFATIGVTFFGAGVISTGSFLTTALISLIQRPQLRNLLHEKPELIPAGVEELLRINLSFADGLPRLATADIQVGDVLVRKGELVLVLLEGANFDPEHFPNPGSIELDRPNPTSHLAFGRGQHFCPGSALGRRHAQIGIEALLKKMPGVDLAVPIDQLVWRTRFQRRIPERLPVLW 396
                                    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       322       332       342       352       362       372       382       392

Chain A from PDB  Type:PROTEIN  Length:394
 aligned with CP121_MYCTU | P9WPP7 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:394
                                    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       322       332       342       352       362       372       382       392    
          CP121_MYCTU     3 ATVLLEVPFSARGDRIPDAVAELRTREPIRKVRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAPRLNALTVPPEVVNNMGNIADAGLRKAVMKAITPKAPGLEQFLRDTANSLLDNLITEGAPADLRNDFADPLATALHCKVLGIPQEDGPKLFRSLSIAFMSSADPIPAAKINWDRDIEYMAGILENPNITTGLMGELSRLRKDPAYSHVSDELFATIGVTFFGAGVISTGSFLTTALISLIQRPQLRNLLHEKPELIPAGVEELLRINLSFADGLPRLATADIQVGDVLVRKGELVLVLLEGANFDPEHFPNPGSIELDRPNPTSHLAFGRGQHFCPGSALGRRHAQIGIEALLKKMPGVDLAVPIDQLVWRTRFQRRIPERLPVLW 396
               SCOP domains d3g5fa_ A: Cyp121 monooxygenase (P450 Mt2)                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3g5fA00 A:3-396 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhh.eeeee.....eeeee.hhhhhhhhhh...eehhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeee...eee..eee....eeeehhhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5f A   3 ATVLLEVPFSARGDRIPDAVAELRTREPIRKVRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAPRLNALTVPPEVVNNMGNIADAGLRKAVMKAITPKAPGLEQFLRDTANSLLDNLITEGAPADLRNDFADPLATALHCKVLGIPQEDGPKLFRSLSIAFMSSADPIPAAKINWDRDIEYMAGILENPNITTGLMGELSRLRKDPAYSHVSDELFATIGVTFFGAGVISTGSFLTTALISLIQRPQLRNLLHEKPELIPAGVEELLRINLSFADGLPRLATADIQVGDVLVRKGELVLVLLEGANFDPEHFPNPGSIELDRPNPTSHLAFGRGQHFCPGSALGRRHAQIGIEALLKKMPGVDLAVPIDQLVWRTRFQRRIPERLPVLW 396
                                    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       322       332       342       352       362       372       382       392

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: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: Cytochrome P450 (323)

Protein domain: Cyp121 monooxygenase (P450 Mt2) (28)

Mycobacterium tuberculosis [TaxId: 1773] (28)

d3g5fa_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Mycobacterium tuberculosis. Organism_taxid: 1773. (3)

3g5fA00

A:3-396

(no "Pfam Domain" information available for 3G5F)

Asymmetric Unit(hide GO term definitions)

Chain A (CP121_MYCTU | P9WPP7)

molecular function
	GO:0070025	carbon monoxide binding	Interacting selectively and non-covalently with carbon monoxide (CO).
	GO:0009975	cyclase activity	Catalysis of a ring closure reaction.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	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:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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:0016125	sterol metabolic process	The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (CP121_MYCTO | P9WPP6)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	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:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:129 - Pro A:130	[ RasMol ]
		Val A:9 - Pro A:10	[ RasMol ]

Biological Units
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