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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCINE CLEAVAGE SYSTEM PROTEIN H FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  13 May 09  (Deposition) - 26 May 09  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Ssgcid, Niaid, Decode, Uw, Sbri, Lipoyl, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Unknown Function, 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 Syste 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GCVH, RV1826, MT1874, MTCY1A11.17C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3HGB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_MYCTO24-106  1A:46-128
GCSH_MYCTU24-106  1A:46-128
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_MYCTO49-78  1A:71-100
GCSH_MYCTU49-78  1A:71-100

(-) Exons   (0, 0)

(no "Exon" information available for 3HGB)

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

    Alignment length:134
                             1                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129    
           GCSH_MYCTO     - -MSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLT 133
               SCOP domains d3hgba_ A: automated matches                                                                                                           SCOP domains
               CATH domains 3hgbA00 A:22-155  [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.hhhhhh.hhhhhh.......eeee.......hhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------BIOTINYL_LIPOYL  PDB: A:46-128 UniProt: 24-106                                     --------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------LIPOYL  PDB: A:71-100         ------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hgb A  22 SMSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLT 155
                                    31        41        51        61        71        81        91       101       111       121       131       141       151    


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

    Alignment length:134
                             1                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129    
           GCSH_MYCTU     - -MSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLT 133
               SCOP domains d3hgba_ A: automated matches                                                                                                           SCOP domains
               CATH domains 3hgbA00 A:22-155  [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.hhhhhh.hhhhhh.......eeee.......hhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------BIOTINYL_LIPOYL  PDB: A:46-128 UniProt: 24-106                                     --------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------LIPOYL  PDB: A:71-100         ------------------------------------------------------- PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hgb A  22 SMSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSEVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLT 155
                                    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)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 4)

Asymmetric/Biological 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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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