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(-) Description

Title :  CRYSTAL STRUCTURE OF "TRUNCATED" HEMOGLOBIN N (HBN) FROM MYCOBACTERIUM TUBERCULOSIS, SOAKED WITH BUTYL-ISOCYANIDE
 
Authors :  M. Milani, A. Pesce, Y. Ouellet, S. Dewilde, J. Friedman, P. Ascenzi, M. Guertin, M. Bolognesi
Date :  22 Jan 04  (Deposition) - 29 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Truncated Hemoglobin, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Milani, A. Pesce, Y. Ouellet, S. Dewilde, J. Friedman, P. Ascenzi, M. Guertin, M. Bolognesi
Heme-Ligand Tunneling In Group I Truncated Hemoglobins
J. Biol. Chem. V. 279 21520 2004
PubMed-ID: 15016811  |  Reference-DOI: 10.1074/JBC.M401320200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN-LIKE PROTEIN HBN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLBN, RV1542C, MT1594, MTCY48.23, MB1569C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: FLAVOHEMOGLOBIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric Unit (6, 10)
No.NameCountTypeFull Name
1CYN2Ligand/IonCYANIDE ION
2HEC1Ligand/IonHEME C
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4K1Ligand/IonPOTASSIUM ION
5NBN1Ligand/IonN-BUTYL ISOCYANIDE
6PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1CYN1Ligand/IonCYANIDE ION
2HEC1Ligand/IonHEME C
3HEM-1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4K-1Ligand/IonPOTASSIUM ION
5NBN1Ligand/IonN-BUTYL ISOCYANIDE
6PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CYN1Ligand/IonCYANIDE ION
2HEC-1Ligand/IonHEME C
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4K-1Ligand/IonPOTASSIUM ION
5NBN-1Ligand/IonN-BUTYL ISOCYANIDE
6PO43Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:33 , GLN A:58 , HEC A:144BINDING SITE FOR RESIDUE CYN A 245
02AC2SOFTWARETYR B:33 , GLN B:58 , HEM B:144BINDING SITE FOR RESIDUE CYN B 345
03AC3SOFTWAREARG B:6 , TYR B:16 , GLY B:21 , HIS B:22 , HOH B:356 , HOH B:402BINDING SITE FOR RESIDUE PO4 B 301
04AC4SOFTWAREARG A:53 , LYS A:57BINDING SITE FOR RESIDUE PO4 A 302
05AC5SOFTWAREGLN B:82 , GLY B:83 , SER B:128 , HOH B:385 , HOH B:391BINDING SITE FOR RESIDUE PO4 B 303
06AC6SOFTWAREGLN A:82 , K A:401 , GLN B:82 , GLY B:83 , ARG B:84BINDING SITE FOR RESIDUE PO4 B 304
07AC7SOFTWAREGLN A:79 , VAL A:80 , GLN A:82 , HOH A:437 , GLY B:83 , PO4 B:304BINDING SITE FOR RESIDUE K A 401
08AC8SOFTWAREPHE 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 , PHE A:91 , VAL A:94 , NBN A:201 , CYN A:245 , HOH B:385BINDING SITE FOR RESIDUE HEC A 144
09AC9SOFTWAREPHE 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 , ARG B:84 , ILE B:86 , PHE B:91 , VAL B:94 , ILE B:119 , LEU B:122 , CYN B:345 , HOH B:347 , HOH B:355 , HOH B:368BINDING SITE FOR RESIDUE HEM B 144
10BC1SOFTWAREPHE A:32 , GLN A:58 , PHE A:62 , VAL A:94 , ILE A:119 , HEC A:144BINDING SITE FOR RESIDUE NBN A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S61)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBIN_FAM_2PS01213 Protozoan/cyanobacterial globins signature.TRHBN_MYCTO61-81
 		  2A:61-81
B:61-81
TRHBN_MYCTU61-81
 		  2A:61-81
B:61-81
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBIN_FAM_2PS01213 Protozoan/cyanobacterial globins signature.TRHBN_MYCTO61-81
 		  1A:61-81
-
TRHBN_MYCTU61-81
 		  1A:61-81
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBIN_FAM_2PS01213 Protozoan/cyanobacterial globins signature.TRHBN_MYCTO61-81
 		  1-
B:61-81
TRHBN_MYCTU61-81
 		  1-
B:61-81

(-) Exons   (0, 0)

(no "Exon" information available for 1S61)

(-) Sequences/Alignments

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:128
 aligned with TRHBN_MYCTO | P9WN24 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
          TRHBN_MYCTO     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
               SCOP domains d1s61a_ A: Protozoan/bacterial hemoglobin                                                                                        SCOP domains
               CATH domains 1s61A00 A:2-129 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
                 1s61 A   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
                                    11        21        31        41        51        61        71        81        91       101       111       121        


Chain A from PDB  Type:PROTEIN  Length:128
 aligned with TRHBN_MYCTU | P9WN25 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
          TRHBN_MYCTU     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
               SCOP domains d1s61a_ A: Protozoan/bacterial hemoglobin                                                                                        SCOP domains
               CATH domains 1s61A00 A:2-129 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
                 1s61 A   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
                                    11        21        31        41        51        61        71        81        91       101       111       121        


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with TRHBN_MYCTO | P9WN24 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
          TRHBN_MYCTO     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSGESTTAPV 136
               SCOP domains d1s61b_ B: Protozoan/bacterial hemoglobin                                                                                               SCOP domains
               CATH domains 1s61B00 B:2-136 Globins                                                                                                                 CATH domains
           Pfam domains (1) ------------Bac_globin-1s61B01 B:14-129                                                                                         ------- Pfam domains (1)
           Pfam domains (2) ------------Bac_globin-1s61B02 B:14-129                                                                                         ------- Pfam domains (2)
         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
                 1s61 B   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSGESTTAPV 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with TRHBN_MYCTU | P9WN25 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
          TRHBN_MYCTU     2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSGESTTAPV 136
               SCOP domains d1s61b_ B: Protozoan/bacterial hemoglobin                                                                                               SCOP domains
               CATH domains 1s61B00 B:2-136 Globins                                                                                                                 CATH domains
           Pfam domains (1) ------------Bac_globin-1s61B01 B:14-129                                                                                         ------- Pfam domains (1)
           Pfam domains (2) ------------Bac_globin-1s61B02 B:14-129                                                                                         ------- Pfam domains (2)
         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
                 1s61 B   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSGESTTAPV 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (13, 19)

Asymmetric Unit(hide GO term definitions)
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.

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.

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  1s61
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  TRHBN_MYCTO | P9WN24
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  TRHBN_MYCTU | P9WN25
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRHBN_MYCTO | P9WN24: 1idr 1rte 1s56 2gkm 2gkn 2gl3 2gln
        TRHBN_MYCTU | P9WN25: 1idr 1rte 1s56 2gkm 2gkn 2gl3 2gln 5ab8

(-) Related Entries Specified in the PDB File

1idr 1rte 1s56