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(-) Description

Title :  HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURE OF BOVINE H-PROTEIN USING A HIGH-PRESSURE CRYOCOOLING METHOD
 
Authors :  A. Higashiura, A. Nakagawa
Date :  19 Jun 13  (Deposition) - 30 Oct 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.86
Chains :  Asym./Biol. Unit :  A
Keywords :  Antiparallel Beta Sheet, Beta Sandwich, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Higashiura, K. Ohta, M. Masaki, M. Sato, K. Inaka, H. Tanaka, A. Nakagawa
High-Resolution X-Ray Crystal Structure Of Bovine H-Protein Using The High-Pressure Cryocooling Method
J. Synchrotron Radiat. V. 20 989 2013
PubMed-ID: 24121354  |  Reference-DOI: 10.1107/S090904951302373X

(-) Compounds

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GCSH
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:25 , LYS A:59 , ALA A:60 , ASN A:87 , LYS A:88 , SER A:89 , CYS A:90 , HOH A:316 , HOH A:328 , HOH A:432 , HOH A:466 , HOH A:467BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREARG A:3 , LYS A:59 , GLU A:113 , HOH A:413 , HOH A:424 , HOH A:505 , HOH A:575BINDING SITE FOR RESIDUE GOL A 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_BOVIN66-148  1A:18-100
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_BOVIN91-120  1A:43-72

(-) Exons   (0, 0)

(no "Exon" information available for 3WDN)

(-) 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    
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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:125
 aligned with GCSH_BOVIN | P20821 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:125
                                    58        68        78        88        98       108       118       128       138       148       158       168     
           GCSH_BOVIN    49 SVRKFTEKHEWVTTENGVGTVGISNFAQEALGDVVYCSLPEVGTKLNKQEEFGALESVKAASELYSPLSGEVTEINKALAENPGLVNKSCYEDGWLIKMTFSNPSELDELMSEEAYEKYIKSIEE 173
               SCOP domains d3wdna_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhh...hhhhhh.......eeeee.hhhhhhhheehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------BIOTINYL_LIPOYL  PDB: A:18-100 UniProt: 66-148                                     ------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------LIPOYL  PDB: A:43-72          ----------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wdn A   1 SVRKFTEKHEWVTTENGVGTVGISNFAQEALGDVVYCSLPEVGTKLNKQEEFGALESVKAASELYSPLSGEVTEINKALAENPGLVNKSCYEDGWLIKMTFSNPSELDELMSEEAYEKYIKSIEE 125
                                    10        20        30        40        50        60        70        80        90       100       110       120
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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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GCSH_BOVIN | P20821)
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.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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UniProtKB/Swiss-Prot
        GCSH_BOVIN | P20821: 3klr

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