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(-) Description

Title :  LOW RESOLUTION 3D STRUCTURE OF C.ELEGANS GLOBIN-LIKE PROTEIN (GLB-1): P3121 CRYSTAL FORM
 
Authors :  E. Geuens, D. Hoogewijs, M. Nardini, E. Vinck, A. Pesce, L. Kiger, A. Fago, L. Tilleman, S. De Henau, M. Marden, R. E. Weber, S. Van Doorslaer, J. Vanfleteren, L. Moens, M. Bolognesi, S. Dewilde
Date :  16 Sep 09  (Deposition) - 21 Apr 10  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metal-Binding, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Geuens, D. Hoogewijs, M. Nardini, E. Vinck, A. Pesce, L. Kiger, A. Fago, L. Tilleman, S. De Henau, M. Marden, R. E. Weber, S. Van Doorslaer, J. Vanfleteren, L. Moens, M. Bolognesi, S. Dewilde
Globin-Like Proteins In Caenorhabditis Elegans: In Vivo Localization, Ligand Binding And Structural Properties.
Bmc Biochem. V. 11 17 2010
PubMed-ID: 20361867  |  Reference-DOI: 10.1186/1471-2091-11-17

(-) Compounds

Molecule 1 - GLOBIN-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY2Ligand/IonOXYGEN MOLECULE
4SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:48 , PHE A:49 , ARG A:65 , GLN A:69 , ARG A:72 , ILE A:73 , ALA A:76 , THR A:97 , ARG A:100 , HIS A:101 , TYR A:104 , MET A:106 , PHE A:114 , OXY A:161BINDING SITE FOR RESIDUE HEM A 160
02AC2SOFTWARETYR A:35 , ILE A:73 , HEM A:160BINDING SITE FOR RESIDUE OXY A 161
03AC3SOFTWARETYR B:48 , ARG B:65 , GLN B:69 , ILE B:73 , ALA B:76 , LEU B:80 , THR B:97 , ARG B:100 , HIS B:101 , TYR B:104 , MET B:106 , TRP B:111 , PHE B:114 , OXY B:161BINDING SITE FOR RESIDUE HEM B 160
04AC4SOFTWAREILE B:73 , HEM B:160BINDING SITE FOR RESIDUE OXY B 161
05AC5SOFTWARESER B:63 , GLU B:64 , ARG B:65BINDING SITE FOR RESIDUE SO4 B1160
06AC6SOFTWAREARG A:72 , LEU A:75 , LEU A:79 , TYR A:93 , TYR B:93 , GLU B:96 , ARG B:100BINDING SITE FOR RESIDUE SO4 A1160
07AC7SOFTWAREHOH B:2024BINDING SITE FOR RESIDUE GOL B1164
08AC8SOFTWAREASN B:4 , ARG B:5 , GLN B:6BINDING SITE FOR RESIDUE GOL B1161
09AC9SOFTWARELYS B:105BINDING SITE FOR RESIDUE GOL B1162
10BC1SOFTWAREHOH B:2025BINDING SITE FOR RESIDUE GOL B1165
11BC2SOFTWAREASN A:4 , ARG A:5 , SER A:63 , ARG A:65 , GOL A:1162BINDING SITE FOR RESIDUE GOL A1161
12BC3SOFTWAREARG A:5 , TYR A:55 , GOL A:1161 , HOH A:2021BINDING SITE FOR RESIDUE GOL A1162

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WTH)

(-) Exons   (0, 0)

(no "Exon" information available for 2WTH)

(-) 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:158
 aligned with GLBH_CAEEL | P30627 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           GLBH_CAEEL     2 SMNRQEISDLCVKSLEGRMVGTEAQNIENGNAFYRYFFTNFPDLRVYFKGAEKYTADDVKKSERFDKQGQRILLACHLLANVYTNEEVFKGYVRETINRHRIYKMDPALWMAFFTVFTGYLESVGCLNDQQKAAWMALGKEFNAESQTHLKNSNLPHV 159
               SCOP domains d2wtha_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains 2wthA00 A:2-159 Globins                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhh.hhhhhh.hhhhhhhhhhhhhh.hhhhhh.hhhhhhhh........hhhhhhhhhhh.........hhhhhhhhhhh.hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wth A   2 SMNRQEISDLCVKSLEGRMVGTEAQNIENGNAFYRYFFTNFPDLRVYFKGAEKYTADDVKKSERFDKQGQRILLACHLLANVYTNEEVFKGYVRETINRHRIYKMDPALWMAFFTVFTGYLESVGSLNDQQKAAWMALGKEFNAESQTHLKNSNLPHV 159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with GLBH_CAEEL | P30627 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           GLBH_CAEEL     2 SMNRQEISDLCVKSLEGRMVGTEAQNIENGNAFYRYFFTNFPDLRVYFKGAEKYTADDVKKSERFDKQGQRILLACHLLANVYTNEEVFKGYVRETINRHRIYKMDPALWMAFFTVFTGYLESVGCLNDQQKAAWMALGKEFNAESQTHLKNSNLPHV 159
               SCOP domains d2wthb_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains 2wthB00 B:2-159 Globins                                                                                                                                        CATH domains
           Pfam domains (1) ---------Globin-2wthB01 B:11-119                                                                                      ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Globin-2wthB02 B:11-119                                                                                      ---------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh........hhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhh.hhhhhhhh........hhhhhhhhhhh.........hhhhhhhhhhh.hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wth B   2 SMNRQEISDLCVKSLEGRMVGTEAQNIENGNAFYRYFFTNFPDLRVYFKGAEKYTADDVKKSERFDKQGQRILLACHLLANVYTNEEVFKGYVRETINRHRIYKMDPALWMAFFTVFTGYLESVGSLNDQQKAAWMALGKEFNAESQTHLKNSNLPHV 159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLBH_CAEEL | P30627)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLBH_CAEEL | P30627: 2wtg

(-) Related Entries Specified in the PDB File

2wtg HIGH RESOLUTION 3D STRUCTURE OF C.ELEGANS GLOBIN-LIKE PROTEIN GLB-1