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Asym./Biol. Unit

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Description

Title :   X-RAY STRUCTURE OF TRUNCATED OXYGEN-AVID HAEMOGLOBIN FROM BACILLUS SUBTILIS

Authors :   A. Ilari, L. Giangiacomo, A. Boffi, E. Chiancone

Date :   20 Feb 04 (Deposition) - 07 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

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

Reference :   L. Giangiacomo, A. Ilari, A. Boffi, V. Morea, E. Chiancone
The Truncated Oxygen-Avid Hemoglobin From Bacillus Subtilis: X-Ray Structure And Ligand Binding Properties
J. Biol. Chem. V. 280 9192 2005
PubMed-ID: 15590662 | Reference-DOI: 10.1074/JBC.M407267200

Compounds

Molecule 1 - YJBI PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	TRUNCATED HEMOGLOBIN

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

Asymmetric/Biological Unit (3, 3)

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

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:25 , GLN A:49 , TRP A:89 , HEM A:700	BINDING SITE FOR RESIDUE CYN A1124
2	AC2	SOFTWARE	HOH A:2049	BINDING SITE FOR RESIDUE CL A1125
3	AC3	SOFTWARE	ILE A:37 , PHE A:38 , THR A:45 , LYS A:48 , GLN A:49 , PHE A:52 , LEU A:53 , TYR A:63 , ARG A:75 , HIS A:76 , ILE A:81 , ALA A:86 , TRP A:89 , CYN A:1124	BINDING SITE FOR RESIDUE HEM A 700

SS Bonds (0, 0)

(no "SS Bond" information available for 1UX8)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1UX8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1UX8)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN_FAM_2	PS01213	Protozoan/cyanobacterial globins signature.	TRHBO_BACSU	52-76	1	A:52-76

Exons (0, 0)

(no "Exon" information available for 1UX8)

Sequences/Alignments

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:119
 aligned with TRHBO_BACSU | O31607 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:119
                                    15        25        35        45        55        65        75        85        95       105       115         
          TRHBO_BACSU     6 NAPYEAIGEELLSQLVDTFYERVASHPLLKPIFPSDLTETARKQKQFLTQYLGGPPLYTEEHGHPMLRARHLPFPITNERADAWLSCMKDAMDHVGLEGEIREFLFGRLELTARHMVNQ 124
               SCOP domains d1ux8a_ A: Protozoan/bacterial hemoglobin                                                                               SCOP domains
               CATH domains 1ux8A00 A:6-124 Globins                                                                                                 CATH domains
               Pfam domains -Bac_globin-1ux8A01 A:7-124                                                                                             Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------GLOBIN_FAM_2  PDB: A:52-7------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ux8 A   6 NAPYEAIGEELLSQLVDTFYERVASHPLLKPIFPSDLTETARKQKQFLTQYLGGPPLYTEEHGHPMLRARHLPFPITNERADAWLSCMKDAMDHVGLEGEIREFLFGRLELTARHMVNQ 124
                                    15        25        35        45        55        65        75        85        95       105       115

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, 1)

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)

Bacillus subtilis [TaxId: 1423] (1)

d1ux8a_

CATH Domains (1, 1)

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)

Bacillus subtilis. Organism_taxid: 1423. (1)

1ux8A00

A:6-124

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Bac_globin (12)

Bacillus subtilis (1)

Bac_globin-1ux8A01

A:7-124

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRHBO_BACSU | O31607)

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).
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.

Visualization

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Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CYN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ux8)

Still Images

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	1ux8
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File