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Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TRHBN TYRB10PHE MUTANT

Authors :   M. Milani, M. Bolognesi

Date :   03 Apr 06 (Deposition) - 19 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Truncated Hemoglobin; Mutant, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Ouellet, M. Milani, M. Couture, M. Bolognesi, M. Guertin
Ligand Interactions In The Distal Heme Pocket Of Mycobacterium Tuberculosis Truncated Hemoglobin N: Roles Of Tyrb10 And Glne11 Residues
Biochemistry V. 45 8770 2006
PubMed-ID: 16846220 | Reference-DOI: 10.1021/BI060112O
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN-LIKE PROTEIN HBN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GLBN
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	TRUNCATED HEMOGLOBIN; TRHBN; FLAVOHEMOGLOBIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CYN	2	Ligand/Ion	CYANIDE ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:79 , VAL A:80 , GLN A:82 , GLY B:83 , HOH B:266	BINDING SITE FOR RESIDUE NA A 137
2	AC2	SOFTWARE	PHE A:33 , GLN A:58 , HEM A:144	BINDING SITE FOR RESIDUE CYN A 145
3	AC3	SOFTWARE	PHE B:33 , GLN B:58 , HEM B:144	BINDING SITE FOR RESIDUE CYN B 145
4	AC4	SOFTWARE	PHE A:45 , PHE A:46 , THR A:49 , ARG A:53 , LEU A:54 , GLN A:58 , PHE A:61 , TYR A:72 , GLY A:74 , ALA A:75 , MET A:77 , VAL A:80 , HIS A:81 , ARG A:84 , ILE A:86 , PHE A:91 , VAL A:94 , VAL A:126 , CYN A:145 , HOH A:182 , HOH A:199 , HOH A:249	BINDING SITE FOR RESIDUE HEM A 144
5	AC5	SOFTWARE	HOH A:215 , LEU B:42 , PHE B:45 , PHE B:46 , THR B:49 , ARG B:53 , LEU B:54 , GLN B:58 , PHE B:61 , TYR B:72 , GLY B:74 , ALA B:75 , MET B:77 , VAL B:80 , HIS B:81 , ILE B:86 , PHE B:91 , VAL B:94 , ILE B:119 , VAL B:126 , CYN B:145 , HOH B:165 , HOH B:284 , HOH B:293	BINDING SITE FOR RESIDUE HEM B 144

(no "SS Bond" information available for 2GKM)

(no "Cis Peptide Bond" information available for 2GKM)

(no "SAP(SNP)/Variant" information available for 2GKM)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN_FAM_2	PS01213	Protozoan/cyanobacterial globins signature.	TRHBN_MYCTO	61-81	2	A:61-81 B:61-81
1	GLOBIN_FAM_2	PS01213	Protozoan/cyanobacterial globins signature.	TRHBN_MYCTU	61-81	2	A:61-81 B:61-81

(no "Exon" information available for 2GKM)

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:127
 aligned with TRHBN_MYCTO | P9WN24 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
          TRHBN_MYCTO     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTS 128
               SCOP domains d2gkma_ A: Protozoan/bacterial hemoglobin                                                                                       SCOP domains
               CATH domains 2gkmA00 A:2-128 Globins                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------GLOBIN_FAM_2         ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gkm A   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFFVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTS 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain A from PDB  Type:PROTEIN  Length:127
 aligned with TRHBN_MYCTU | P9WN25 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
          TRHBN_MYCTU     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTS 128
               SCOP domains d2gkma_ A: Protozoan/bacterial hemoglobin                                                                                       SCOP domains
               CATH domains 2gkmA00 A:2-128 Globins                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------GLOBIN_FAM_2         ----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gkm A   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFFVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTS 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with TRHBN_MYCTO | P9WN24 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
          TRHBN_MYCTO     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVT 127
               SCOP domains d2gkmb_ B: Protozoan/bacterial hemoglobin                                                                                      SCOP domains
               CATH domains 2gkmB00 B:2-127 Globins                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------GLOBIN_FAM_2         ---------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gkm B   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFFVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVT 127
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with TRHBN_MYCTU | P9WN25 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
          TRHBN_MYCTU     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVT 127
               SCOP domains d2gkmb_ B: Protozoan/bacterial hemoglobin                                                                                      SCOP domains
               CATH domains 2gkmB00 B:2-127 Globins                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------GLOBIN_FAM_2         ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gkm B   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFFVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVT 127
                                    11        21        31        41        51        61        71        81        91       101       111       121

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: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Truncated hemoglobin (27)

Protein domain: Protozoan/bacterial hemoglobin (22)

Mycobacterium tuberculosis, HbN [TaxId: 1773] (8)

1a	d2gkma_	A:
1b	d2gkmb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Mycobacterium tuberculosis. Organism_taxid: 1773. (8)

1a	2gkmA00	A:2-128
1b	2gkmB00	B:2-127

(no "Pfam Domain" information available for 2GKM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TRHBN_MYCTU | P9WN25)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008941	nitric oxide dioxygenase activity	Catalysis of the reaction: 2 NO + 2 O2 + NADPH + H+ = 2 nitrate + NADP+.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0051410	detoxification of nitrogen compound	Any process that reduces or removes the toxicity of nitrogenous compounds which are dangerous or toxic. This includes the aerobic conversion of toxic compounds to harmless substances.
	GO:0052060	evasion or tolerance by symbiont of host-produced nitric oxide	The process in which an organism avoids the effects of nitric oxide produced as a defense response by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0046210	nitric oxide catabolic process	The chemical reactions and pathways resulting in the breakdown of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
	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:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A,B (TRHBN_MYCTO | P9WN24)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gkm)

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	2gkm
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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