3HX9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF HEME-DEGRADER, MHUD (RV3592), FROM MYCOBACTERIUM TUBERCULOSIS WITH TWO HEMES BOUND IN ITS ACTIVE SITE

Authors :   N. Chim, T. Q. Nguyen, A. Iniguez, C. W. Goulding

Date :   19 Jun 09 (Deposition) - 01 Dec 09 (Release) - 02 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Di-Heme, Beta Barrel, Dimer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Chim, A. Iniguez, T. Q. Nguyen, C. W. Goulding
Unusual Diheme Conformation Of The Heme-Degrading Protein From Mycobacterium Tuberculosis
J. Mol. Biol. V. 395 595 2009
PubMed-ID: 19917297 | Reference-DOI: 10.1016/J.JMB.2009.11.025

Molecule 1 - PROTEIN RV3592
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MT3698, RV3592, TB11.2
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:22 , ARG A:26 , ALA A:29 , TRP A:66 , ALA A:67 , ALA A:71 , HIS A:75 , ASN A:81 , HEM A:200	BINDING SITE FOR RESIDUE HEM A 300
2	AC2	SOFTWARE	ASN A:7 , PHE A:23 , VAL A:53 , HEM A:200	BINDING SITE FOR RESIDUE CL A 301
3	AC3	SOFTWARE	ASN A:7 , ARG A:22 , PHE A:23 , VAL A:30 , PHE A:39 , THR A:55 , PHE A:63 , ILE A:72 , ASN A:81 , PRO A:82 , VAL A:83 , ALA A:84 , GLY A:86 , HEM A:300 , CL A:301	BINDING SITE FOR RESIDUE HEM A 200
4	AC4	SOFTWARE	ARG B:22 , ARG B:26 , ALA B:29 , TRP B:66 , ALA B:67 , ALA B:71 , ALA B:74 , HIS B:75 , ALA B:80 , PRO B:82 , HOH B:125 , HEM B:200	BINDING SITE FOR RESIDUE HEM B 300
5	AC5	SOFTWARE	ASN B:7 , PHE B:23 , VAL B:53 , HEM B:200	BINDING SITE FOR RESIDUE CL B 301
6	AC6	SOFTWARE	ASN B:7 , ARG B:22 , PHE B:23 , VAL B:30 , PHE B:39 , THR B:55 , ILE B:72 , PRO B:82 , VAL B:83 , ALA B:84 , GLY B:86 , HOH B:184 , HEM B:300 , CL B:301	BINDING SITE FOR RESIDUE HEM B 200

(no "SS Bond" information available for 3HX9)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:81	-	Pro A:82

(no "SAP(SNP)/Variant" information available for 3HX9)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABM	PS51725	ABM domain profile.	MHUD_MYCTO	3-92	2	A:3-92 B:3-92
1	ABM	PS51725	ABM domain profile.	MHUD_MYCTU	3-92	2	A:3-92 B:3-92

(no "Exon" information available for 3HX9)

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:101
 aligned with MHUD_MYCTO | P9WKH2 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:101
                                    11        21        31        41        51        61        71        81        91       101 
           MHUD_MYCTO     2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVGGTG 102
               SCOP domains d3hx9a_ A: automated matches                                                                          SCOP domains
               CATH domains 3hx9A00 A:2-102  [code=3.30.70.900, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.........eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh............eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -ABM  PDB: A:3-92 UniProt: 3-92                                                            ---------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3hx9 A   2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVGGTG 102
                                    11        21        31        41        51        61        71        81        91       101

Chain A from PDB  Type:PROTEIN  Length:101
 aligned with MHUD_MYCTU | P9WKH3 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:101
                                    11        21        31        41        51        61        71        81        91       101 
           MHUD_MYCTU     2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVGGTG 102
               SCOP domains d3hx9a_ A: automated matches                                                                          SCOP domains
               CATH domains 3hx9A00 A:2-102  [code=3.30.70.900, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.........eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh............eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ABM  PDB: A:3-92 UniProt: 3-92                                                            ---------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3hx9 A   2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVGGTG 102
                                    11        21        31        41        51        61        71        81        91       101

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with MHUD_MYCTO | P9WKH2 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:98
                                    11        21        31        41        51        61        71        81        91        
           MHUD_MYCTO     2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVG  99
               SCOP domains d3hx9b_ B: automated matches                                                                       SCOP domains
               CATH domains 3hx9B00 B:2-99  [code=3.30.70.900, no name defined]                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.........eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh............eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -ABM  PDB: B:3-92 UniProt: 3-92                                                            ------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3hx9 B   2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVG  99
                                    11        21        31        41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with MHUD_MYCTU | P9WKH3 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:98
                                    11        21        31        41        51        61        71        81        91        
           MHUD_MYCTU     2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVG  99
               SCOP domains d3hx9b_ B: automated matches                                                                       SCOP domains
               CATH domains 3hx9B00 B:2-99  [code=3.30.70.900, no name defined]                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.........eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh............eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ABM  PDB: B:3-92 UniProt: 3-92                                                            ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3hx9 B   2 PVVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAAHAGHRANPVATGASLLEFEVVLDVG  99
                                    11        21        31        41        51        61        71        81        91

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Dimeric alpha+beta barrel (122)

Family: automated matches (41)

Protein domain: automated matches (41)

Mycobacterium tuberculosis [TaxId: 1773] (1)

1a	d3hx9a_	A:
1b	d3hx9b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.900, no name defined] (47)

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv. (1)

1a	3hx9A00	A:2-102
1b	3hx9B00	B:2-99

(no "Pfam Domain" information available for 3HX9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MHUD_MYCTU | P9WKH3)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0004392	heme oxygenase (decyclizing) activity	Catalysis of the reaction: heme + 3 donor-H2 + 3 O2 = biliverdin + Fe2+ + CO + 3 acceptor + 3 H2O.
	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.
biological process
	GO:0042167	heme catabolic process	The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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,B (MHUD_MYCTO | P9WKH2)

molecular function
	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.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:81 - Pro A:82	[ RasMol ]

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	3hx9
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UniProtKB/Swiss-Prot
	MHUD_MYCTO \| P9WKH2	:	4nl5
	MHUD_MYCTU \| P9WKH3	:	4nl5 5uq4

(no "Related Entries Specified in the PDB File" available for 3HX9)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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