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(-) Description

Title :  X-RAY STRUCTURE OF CYANIDE DERIVATIVE OF TRUNCATED HEMOGLOBIN N (TRHBN) FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  M. Milani, M. Guertin, A. Boffi, G. Antonini, A. Bocedi, M. Mattu, M. Bolognesi, P. Ascenzi
Date :  10 Dec 03  (Deposition) - 27 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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, Y. Ouellet, H. Ouellet, M. Guertin, A. Boffi, G. Antonini, A. Bocedi, M. Mattu, M. Bolognesi, P. Ascenzi
Cyanide Binding To Truncated Hemoglobins: A Crystallographic And Kinetic Study
Biochemistry V. 43 5213 2004
PubMed-ID: 15122887  |  Reference-DOI: 10.1021/BI049870+
(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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CYN2Ligand/IonCYANIDE ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1CYN1Ligand/IonCYANIDE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CYN1Ligand/IonCYANIDE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:33 , GLN A:58 , HEM A:144BINDING SITE FOR RESIDUE CYN A 445
02AC2SOFTWARETYR B:33 , GLN B:58 , HIS B:81 , HEM B:144BINDING SITE FOR RESIDUE CYN B 446
03AC3SOFTWAREGLY B:2 , ARG B:6 , TYR B:16 , HOH B:516 , HOH B:530BINDING SITE FOR RESIDUE SO4 B 301
04AC4SOFTWAREALA A:75 , HOH A:510 , ARG B:10 , GLN B:41 , HIS B:89 , HOH B:479 , HOH B:545BINDING SITE FOR RESIDUE SO4 B 302
05AC5SOFTWAREGLY A:2 , SER A:5 , LYS A:9 , HOH A:502 , PRO B:108 , SER B:109BINDING SITE FOR RESIDUE SO4 A 303
06AC6SOFTWAREARG A:10 , GLN A:41 , HIS A:89 , GLN B:82BINDING SITE FOR RESIDUE SO4 A 304
07AC7SOFTWAREGLY A:2 , LEU A:3 , LEU A:4 , SER A:5BINDING SITE FOR RESIDUE SO4 A 305
08AC8SOFTWAREPRO A:108 , SER A:109 , GLU A:110 , HOH A:517BINDING SITE FOR RESIDUE SO4 A 306
09AC9SOFTWAREGLY B:2 , LEU B:3 , LEU B:4 , SER B:5BINDING SITE FOR RESIDUE SO4 B 307
10BC1SOFTWAREARG A:84 , GLY B:83 , ARG B:84 , GLY B:85BINDING SITE FOR RESIDUE SO4 A 308
11BC2SOFTWAREPHE 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 , ILE A:86 , PHE A:91 , VAL A:94 , VAL A:126 , CYN A:445 , HOH A:528 , HOH A:535BINDING SITE FOR RESIDUE HEM A 144
12BC3SOFTWAREHOH A:454 , 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 , HIS B:81 , ARG B:84 , ILE B:86 , HIS B:90 , PHE B:91 , VAL B:94 , ILE B:119 , CYN B:446 , HOH B:504 , HOH B:511BINDING SITE FOR RESIDUE HEM B 144

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1RTE)

(-) 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 d1rtea_ A: Protozoan/bacterial hemoglobin                                                                                        SCOP domains
               CATH domains 1rteA00 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
                 1rte 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 d1rtea_ A: Protozoan/bacterial hemoglobin                                                                                        SCOP domains
               CATH domains 1rteA00 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
                 1rte A   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
                                    11        21        31        41        51        61        71        81        91       101       111       121        


Chain B 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 d1rteb_ B: Protozoan/bacterial hemoglobin                                                                                        SCOP domains
               CATH domains 1rteB00 B:2-129 Globins                                                                                                          CATH domains
           Pfam domains (1) ------------Bac_globin-1rteB01 B:14-129                                                                                          Pfam domains (1)
           Pfam domains (2) ------------Bac_globin-1rteB02 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
                 1rte B   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
                                    11        21        31        41        51        61        71        81        91       101       111       121        


Chain B 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 d1rteb_ B: Protozoan/bacterial hemoglobin                                                                                        SCOP domains
               CATH domains 1rteB00 B:2-129 Globins                                                                                                          CATH domains
           Pfam domains (1) ------------Bac_globin-1rteB01 B:14-129                                                                                          Pfam domains (1)
           Pfam domains (2) ------------Bac_globin-1rteB02 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
                 1rte B   2 GLLSRLRKREPISIYDKIGGHEAIEVVVEDFYVRVLADDQLSAFFSGTNMSRLKGKQVEFFAAALGGPEPYTGAPMKQVHQGRGITMHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVTSG 129
                                    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 '|'

 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_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.

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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 1s56 1s61 2gkm 2gkn 2gl3 2gln
        TRHBN_MYCTU | P9WN25: 1idr 1s56 1s61 2gkm 2gkn 2gl3 2gln 5ab8

(-) Related Entries Specified in the PDB File

1idr CRYSTAL STRUCTURE OF THE TRUNCATED-HEMOGLOBIN-N FROM MYCOBACTERIUM TUBERCULOSIS