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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYCINE CLEAVAGE SYSTEM H PROTEIN (GCVH) FROM MYCOBACTERIUM MARINUM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  27 Sep 11  (Deposition) - 05 Oct 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GCVH_1, GCVH1, MMAR_0209
    Organism Scientific: MYCOBACTERIUM MARINUM
    Organism Taxid: 216594
    Strain: ATCC BAA-535 / M
    Synonym: GCVH

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):  B  
Biological Unit 5 (1x):   C 
Biological Unit 6 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER B:60 , SER B:82 , HOH B:175 , SER D:60 , SER D:82 , HOH D:138 , HOH D:152BINDING SITE FOR RESIDUE ACT B 134
02AC2SOFTWARESER A:60 , SER A:82 , HOH A:151 , SER C:60 , SER C:82 , HOH C:156BINDING SITE FOR RESIDUE ACT A 134
03AC3SOFTWAREALA A:43 , LYS A:72 , THR A:73 , EDO A:137 , HOH A:162 , ASP C:15 , SER C:75BINDING SITE FOR RESIDUE EDO A 135
04AC4SOFTWAREASP A:15 , GLU A:17 , VAL A:68 , SER A:75 , ASP A:76 , LEU A:77 , ILE A:78 , EDO A:137BINDING SITE FOR RESIDUE EDO A 136
05AC5SOFTWAREASP B:15 , GLU B:17 , SER B:75 , ASP B:76 , HOH B:178 , HOH D:167BINDING SITE FOR RESIDUE EDO B 135
06AC6SOFTWARESER A:75 , EDO A:135 , EDO A:136 , HOH A:177 , ALA C:43BINDING SITE FOR RESIDUE EDO A 137
07AC7SOFTWAREALA B:43 , LYS B:72 , THR B:73 , HOH B:155 , SER D:75BINDING SITE FOR RESIDUE EDO B 136
08AC8SOFTWARESER C:11 , ALA C:22 , GLY C:24BINDING SITE FOR RESIDUE EDO C 134
09AC9SOFTWARELYS A:72 , HOH A:145 , LYS B:72 , VAL B:74 , HOH B:146 , ASP C:76 , ASP D:76BINDING SITE FOR RESIDUE PEG C 135
10BC1SOFTWAREGLU A:67 , ASP A:76 , ASP B:76 , HOH B:158 , LYS C:72 , LYS D:72 , VAL D:74 , HOH D:169BINDING SITE FOR RESIDUE PEG A 138

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TZU)

(-) Exons   (0, 0)

(no "Exon" information available for 3TZU)

(-) 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:127
 aligned with B2HKH2_MYCMM | B2HKH2 from UniProtKB/TrEMBL  Length:134

    Alignment length:127
                                    15        25        35        45        55        65        75        85        95       105       115       125       
         B2HKH2_MYCMM     6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
               SCOP domains d3tzua_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eee............eeeeehhhhhhhhh.eeeee......ee....eeeeeee..eeeeee..eeeeeeeehhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzu A   6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
                                    15        25        35        45        55        65        75        85        95       105       115       125       


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with B2HKH2_MYCMM | B2HKH2 from UniProtKB/TrEMBL  Length:134

    Alignment length:127
                                    15        25        35        45        55        65        75        85        95       105       115       125       
         B2HKH2_MYCMM     6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
               SCOP domains d3tzub_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eee............eeeeehhhhhhhhh.eeeee......ee....eeeeeee..eeeeee..eeeeeeeehhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzu B   6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
                                    15        25        35        45        55        65        75        85        95       105       115       125       


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with B2HKH2_MYCMM | B2HKH2 from UniProtKB/TrEMBL  Length:134

    Alignment length:127
                                    15        25        35        45        55        65        75        85        95       105       115       125       
         B2HKH2_MYCMM     6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
               SCOP domains d3tzuc_ C: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eee............eeeeehhhhhhhhh.eeeee......ee....eeeeeee..eeeeee..eeeeeeeehhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzu C   6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
                                    15        25        35        45        55        65        75        85        95       105       115       125       


Chain D from PDB  Type:PROTEIN  Length:127
 aligned with B2HKH2_MYCMM | B2HKH2 from UniProtKB/TrEMBL  Length:134

    Alignment length:127
                                    15        25        35        45        55        65        75        85        95       105       115       125       
         B2HKH2_MYCMM     6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
               SCOP domains d3tzud_ D: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eee............eeeeehhhhhhhhh.eeeee......ee....eeeeeee..eeeeee..eeeeeeeehhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzu D   6 IPGDRSYTADHEWIDIAPGAATPDGPVRVGITSVAVEALGDLVFVQLPEVGETVSAGESCGEVESTKTVSDLIAPASGQIVEVNTAAVDDPATIATDPYGAGWLYSVQPTAVGELLTASEYAGQNGL 132
                                    15        25        35        45        55        65        75        85        95       105       115       125
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TZU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B2HKH2_MYCMM | B2HKH2)
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

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(-) Related Entries Specified in the PDB File

3hgb CRYSTAL STRUCTURE OF GLYCINE CLEAVAGE SYSTEM PROTEIN H FROM MYCOBACTERIUM TUBERCULOSIS
3ift CRYSTAL STRUCTURE OF GLYCINE CLEAVAGE SYSTEM PROTEIN H FROM MYCOBACTERIUM TUBERCULOSIS, USING X-RAYS FROM THE COMPACT LIGHT SOURCE. RELATED ID: MYMAA.01046.B RELATED DB: TARGETDB
3mxu CRYSTAL STRUCTURE OF GLYCINE CLEAVAGE SYSTEM PROTEIN H FROM BARTONELLA HENSELAE