Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCINE CLEAVAGE SYSTEM PROTEIN H FROM MYCOBACTERIUM TUBERCULOSIS, USING X-RAYS FROM THE COMPACT LIGHT SOURCE.
 
Authors :  T. E. Edwards, J. Abendroth, B. Staker, C. Mayer, I. Phan, A. Kelley, E. A D. Leibly, J. Rifkin, R. Loewen, R. D. Ruth, L. J. Stewart, Accelerated Technologies Center For Gene To 3D Structure (Atcg3D)
Date :  25 Jul 09  (Deposition) - 11 Aug 09  (Release) - 28 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Niaid, Decode, Uw, Sbri, Glycine Cleavage System, Structural Genomics, Psi-2, Protein Structure Initiative, Accelerated Technologies Center For Gene To 3D Structure, Atcg3D, Seattle Structural Genomics Center For Infectious Disease, Lipoyl, Methylamine Binding Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, M. S. Mccormick, T. E. Edwards, B. Staker, R. Loewen, M. Gifford, J. Rifkin, C. Mayer, W. Guo, Y. Zhang, P. Myler, A. Kelley, E. Analau, S. N. Hewitt, A. J. Napuli, P. Kuhn, R. D. Ruth, L. J. Stewart
X-Ray Structure Determination Of The Glycine Cleavage System Protein H Of Mycobacterium Tuberculosis Using An Inverse Compton Synchrotron X-Ray Source.
J. Struct. Funct. Genom. V. 11 91 2010
PubMed-ID: 20364333  |  Reference-DOI: 10.1007/S10969-010-9087-6

(-) Compounds

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GCHV, GCVH, MT1874, MTCY1A11.17C, RV1826
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3IFT)

(-) Sites  (0, 0)

(no "Site" information available for 3IFT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IFT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IFT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IFT)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_MYCTO24-106  1A:24-106
GCSH_MYCTU24-106  1A:24-106
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_MYCTO49-78  1A:49-78
GCSH_MYCTU49-78  1A:49-78
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_MYCTO24-106  1A:24-106
GCSH_MYCTU24-106  1A:24-106
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_MYCTO49-78  1A:49-78
GCSH_MYCTU49-78  1A:49-78
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_MYCTO24-106  2A:24-106
GCSH_MYCTU24-106  2A:24-106
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_MYCTO49-78  2A:49-78
GCSH_MYCTU49-78  2A:49-78

(-) Exons   (0, 0)

(no "Exon" information available for 3IFT)

(-) 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:136
 aligned with GCSH_MYCTO | P9WN54 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:136
                              1                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128      
           GCSH_MYCTO     - --MSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLTE 134
               SCOP domains d3ifta_ A: automated matches                                                                                                             SCOP domains
               CATH domains 3iftA00 A:-1-134  [code=2.40.50.100, no name defined]                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....eeeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhhhhhhhhh.......eeee.......hhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------BIOTINYL_LIPOYL  PDB: A:24-106 UniProt: 24-106                                     ---------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------LIPOYL  PDB: A:49-78          -------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ift A  -1 HHVSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLTE 134
                                     8        18        28        38        48        58        68        78        88        98       108       118       128      


Chain A from PDB  Type:PROTEIN  Length:136
 aligned with GCSH_MYCTU | P9WN55 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:136
                              1                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128      
           GCSH_MYCTU     - --MSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLTE 134
               SCOP domains d3ifta_ A: automated matches                                                                                                             SCOP domains
               CATH domains 3iftA00 A:-1-134  [code=2.40.50.100, no name defined]                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....eeeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhhhhhhhhh.......eeee.......hhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------BIOTINYL_LIPOYL  PDB: A:24-106 UniProt: 24-106                                     ---------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------LIPOYL  PDB: A:49-78          -------------------------------------------------------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ift A  -1 HHVSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLTE 134
                                     8        18        28        38        48        58        68        78        88        98       108       118       128
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IFT)

(-) Gene Ontology  (2, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (GCSH_MYCTO | P9WN54)
biological process
    GO:0019464    glycine decarboxylation via glycine cleavage system    The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
cellular component
    GO:0005960    glycine cleavage complex    A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.

Chain A   (GCSH_MYCTU | P9WN55)
biological process
    GO:0019464    glycine decarboxylation via glycine cleavage system    The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
cellular component
    GO:0005960    glycine cleavage complex    A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3ift)
 
  Sites
(no "Sites" information available for 3ift)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ift)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ift
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GCSH_MYCTO | P9WN54
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  GCSH_MYCTU | P9WN55
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GCSH_MYCTO | P9WN54
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GCSH_MYCTU | P9WN55
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GCSH_MYCTO | P9WN54: 3hgb
        GCSH_MYCTU | P9WN55: 3hgb 5exk

(-) Related Entries Specified in the PDB File

3hgb RELATED ID: MYTUD.01046.A RELATED DB: TARGETDB