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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METHANOCALDOCOCCUS JANNASCHII G1PDH
 
Authors :  V. Carbone, R. S. Ronimus, L. R. Schofield, A. J. Sutherland-Smith
Date :  30 Sep 14  (Deposition) - 22 Jul 15  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Oxidoreductase, Rossman Fold, Metal Ion Binding, Nadp(H) Binding, Zn Binding, Sn-Glycerol-1-Phosphate Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Carbone, L. R. Schofield, Y. Zhang, C. Sang, D. Dey, I. M. Hannus, W. F. Martin, A. J. Sutherland-Smith, R. S. Ronimus
Structure And Evolution Of The Archaeal Lipid Synthesis Enzyme Sn-Glycerol-1-Phosphate Dehydrogenase.
J. Biol. Chem. V. 290 21690 2015
PubMed-ID: 26175150  |  Reference-DOI: 10.1074/JBC.M115.647461

(-) Compounds

Molecule 1 - GLYCEROL-1-PHOSPHATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.261
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151D
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EGSA, MJ0712
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
    Synonym: G1P DEHYDROGENASE, G1PDH, ENANTIOMERIC GLYCEROPHOSPHATE SYNTHASE, SN-GLYCEROL-1-PHOSPHATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:105 , ASP A:148 , SER A:151 , ASN A:152 , ALA A:221BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:148 , HIS A:226 , HIS A:247BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREASP B:105 , ASP B:148 , SER B:151 , ASN B:152 , ALA B:221BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWAREASP B:148 , HIS B:226 , HIS B:247BINDING SITE FOR RESIDUE ZN B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RGV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:116 -Pro A:117
2Gln B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RGV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RGV)

(-) Exons   (0, 0)

(no "Exon" information available for 4RGV)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee.hhhhhhhhhhhhh....eeeeehhhhhhhh.....eeehhhhhhh........eeeeeehhhhhhhhhhhhhhhh..eeeee....hhhhh..ee....ee.....eeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rgv A   2 IIVTPRYTIIEDGAINKIEEILKKLNLKNPLVITGKNTKKYCRFFYDIVYYDEILNNLKKYTAYDCVIGIGGGRSIDTGKYLAYKLGIPFISVPTTASNDGIASPIVSQPSFMVDAPIAIIADTEIIKKSPRRLLSAGMGDIVSNITAVLDWKLAYKEKGEKYSESSAIFSKTIAKELISYVLNSDLSEYHNKLVKALVGSGIAIAIANSSRPASGSEHLFSHALDKLKEEYNLNINSLHGEQCGIGTIMMSYLHEKENKKLSGLHEKIKMSLKKVDAPTTAKELGFDEDIIIEALTMAHKIRNRWTILRDGLSREEARKLAEETGVI 335
                                    11        21        31        41        51      ||65        75        85        95       105       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327        
                                                                                   58|                                               113|                                                                                                                                                                                                                           
                                                                                    63                                                116                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee.hhhhhhhhhhhhh....eeeeehhhhh........eeehhhhhh...........eeeeeehhhhhhhhhhhhhhhh..eeeee....hhhhh..ee......ee.....eeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rgv B   1 MIIVTPRYTIIEDGAINKIEEILKKLNLKNPLVITGKNTKKYCRFFYDIVYYDEILNNLELKKYTAYDCVIGIGGGRSIDTGKYLAYKLGIPFISVPTTASNDGIASPIVSIRQPSFMVDAPIAIIADTEIIKKSPRRLLSAGMGDIVSNITAVLDWKLAYKEKGEKYSESSAIFSKTIAKELISYVLNSDLSEYHNKLVKALVGSGIAIAIANSSRPASGSEHLFSHALDKLKEEYNLNINSLHGEQCGIGTIMMSYLHEKENKKLSGLHEKIKMSLKKVDAPTTAKELGFDEDIIIEALTMAHKIRNRWTILRDGLSREEARKLAEETGVI 335
                                    10        20        30        40        50        60|       72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   
                                                                                      60|                                                                                                                                                                                                                                                                                
                                                                                       63
   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  (0, 0)

(no "SCOP Domain" information available for 4RGV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RGV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RGV)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:116 - Pro A:117   [ RasMol ]  
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  4rgv
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  G1PDH_METJA | Q58122
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  1.1.1.261
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 Related Entries

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

UniProtKB/Swiss-Prot
        G1PDH_METJA | Q58122: 4rfl 4rgq

(-) Related Entries Specified in the PDB File

4rfl THE SAME PROTEIN COMPLEXED WITH NADPH
4rgq THE SAME PROTEIN COMPLEXED WITH NADPH AND DHAP