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(-) Description

Title :  CRYSTAL STRUCTURE OF LIPOYLATED E. COLI H-PROTEIN (REDUCED FORM)
 
Authors :  K. Okamura-Ikeda, N. Maita
Date :  04 Dec 09  (Deposition) - 07 Apr 10  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycine Cleavage System, Lipoyl, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okamura-Ikeda, H. Hosaka, N. Maita, K. Fujiwara, A. C. Yoshizawa, A. Nakagawa, H. Taniguchi
Crystal Structure Of Aminomethyltransferase In Complex With Dihydrolipoyl-H-Protein Of The Glycine Cleavage System: Implications For Recognition Of Lipoyl Protein Substrate, Disease-Related Mutations, And Reaction Mechanism
J. Biol. Chem. V. 285 18684 2010
PubMed-ID: 20375021  |  Reference-DOI: 10.1074/JBC.M110.110718

(-) Compounds

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GCVH
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12 SUBSTR. W3110

 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.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3LA21Mod. Amino AcidN~6~-[(6R)-6,8-DISULFANYLOCTANOYL]-L-LYSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , LEU A:44 , ASP A:127 , HOH A:170 , HOH A:171 , HOH A:174BINDING SITE FOR RESIDUE CA A 129
2AC2SOFTWAREGLU A:94 , PRO A:95 , TYR A:96BINDING SITE FOR RESIDUE CL A 130

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AB9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AB9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AB9)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_ECOLI24-106  1A:23-105
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_ECOLI49-78  1A:48-77

(-) Exons   (0, 0)

(no "Exon" information available for 3AB9)

(-) 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:127
 aligned with GCSH_ECOLI | P0A6T9 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
           GCSH_ECOLI     3 NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 129
               SCOP domains d3ab9a_ A: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 3ab9A00 A:2-128  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeee.....eeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhh.hhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------BIOTINYL_LIPOYL  PDB: A:23-105 UniProt: 24-106                                     ----------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------LIPOYL  PDB: A:48-77          --------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ab9 A   2 NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVkAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 128
                                    11        21        31        41        51        61  |     71        81        91       101       111       121       
                                                                                         64-LA2
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  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 3AB9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GCSH_ECOLI | P0A6T9)
molecular function
    GO:0031405    lipoic acid binding    Interacting selectively and non-covalently with lipoic acid, 1,2-dithiolane-3-pentanoic acid.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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_ECOLI | P0A6T9: 3a7a 3a7l 3a8i 3a8j 3a8k

(-) Related Entries Specified in the PDB File

1hpc H-PROTEIN FROM PISUM SATIVUM
1htp H-PROTEIN FROM PISUM SATIVUM
3a8i E. COLI T-PROTEIN IN COMPLEX WITH DIHYDROLIPOATE-BEARING E. COLI H-PROTEIN AND 5-CH3-THF
3a8j E. COLI T-PROTEIN IN COMPLEX WITH DIHYDROLIPOATE-BEARING E. COLI H-PROTEIN
3a8k E. COLI T-PROTEIN MUTANT D97N IN COMPLEX WITH DIHYDROLIPOATE-BEARING E. COLI H-PROTEIN