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(-) Description

Title :  GLUTAMYL-TRNA REDUCTASE FROM METHANOPYRUS KANDLERI
 
Authors :  J. Moser, W. -D. Schubert, V. Beier, I. Bringemeier, D. Jahn, D. W. Heinz
Date :  05 Nov 01  (Deposition) - 04 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Reductase, Trna-Dependent Tetrapyrrole Biosynthesis, Glutamyl Trna- Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Moser, W. -D. Schubert, V. Beier, I. Bringemeier, D. Jahn, D. W. Heinz
V-Shaped Structure Of Glutamyl-Trna Reductase, The First Enzyme Of Trna-Dependent Tetrapyrrole Biosynthesis.
Embo J. V. 20 6583 2001
PubMed-ID: 11726494  |  Reference-DOI: 10.1093/EMBOJ/20.23.6583

(-) Compounds

Molecule 1 - GLUTAMYL-TRNA REDUCTASE
    Chains: A
    EC Number: 1.2.1.-
    Fragment: WHOLE MOLECULE, RESIDUES 1-404
    Mutation: YES
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 2320
    Other Details: DSM 6324, GERMAN COLLECTION OF MICROORGANISMS (DSM)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GMC1Ligand/Ion(2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2GLU2Mod. Amino AcidGLUTAMIC ACID
3GMC2Ligand/Ion(2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , GLU A:25 , SER A:48 , GLU A:101 , GLU A:1406 , HOH A:2346BINDING SITE FOR RESIDUE GMC A1405
2AC2SOFTWARETHR A:47 , ASN A:49 , ARG A:50 , SER A:94 , GLU A:99 , GLU A:101 , ILE A:102 , GLN A:105 , GMC A:1405 , HOH A:2055 , HOH A:2347BINDING SITE FOR RESIDUE GLU A1406
3AC3SOFTWAREGLU A:99 , GLN A:100 , ALA A:147 , VAL A:148 , SER A:149 , SER A:152 , ARG A:300 , HOH A:2349 , HOH A:2350 , HOH A:2352 , HOH A:2353 , HOH A:2354BINDING SITE FOR RESIDUE CIT A1407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GPJ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:267 -Pro A:268
2Lys A:354 -Thr A:355
3Met A:382 -Glu A:383

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GPJ)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTRPS00747 Glutamyl-tRNA reductase signature.HEM1_METKA84-107  1A:84-107
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTRPS00747 Glutamyl-tRNA reductase signature.HEM1_METKA84-107  2A:84-107

(-) Exons   (0, 0)

(no "Exon" information available for 1GPJ)

(-) 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:400
 aligned with HEM1_METKA | Q9UXR8 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                             404 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400   | 
          HEM1_METKA      1 MEDLVCVGITHKEAEVEELEKARFESDEAVRDIVESFGLSGCVLLQTCNRVEVYASGARDRAEELGDLIHDDAWVKRGSEAVRHLFRVACGLESMMVGEQEILRQVKKAYDRAARLGTLDEALKIVFRRAINLGKRAREETRISEGAVSIGSAAVELAERELGSLHDKTVLVVGAGEMGKTVAKSLVDRGVRAVLVANRTYERAVELARDLGGEAVRFDELVDHLARSDVVVSATAAPHPVIHVDDVREALRKRDRRSPILIIDIANPRDVEEGVENIEDVEVRTIDDLRVIARENLERRRKEIPKVEKLIEEELSTVEEELEKLKERRLVADVAKSLHEIKDRELERALRRLKTGDPENVLQDFAEAYTKRLINVLTSAIMELPDEYRRAACRALRRASELNG-    -
               SCOP domains d1gpja3 A:1-143 Glutamyl tRNA-reductase catalytic, N-terminal domain                                                                           d1gpja2 A:144-302 Glutamyl tRNA-reductase middle domain                                                                                                        d1gpja1 A:303-404 Glutamyl tRNA-reductase dimerizatio     n domain                                    - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------1gpjA02 A:146-299 NAD(P)-binding Rossmann-like Domain                                                                                                     ---------------1gpjA03 A:315-404 Glutamyl-tRNA reductase       dimerization domain, domain 3             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhh....hhhhhhhhhh...eeeeeee..eeeeeee....hhhhhhhh.....eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee.hhhhhhhhhhh..eeee.........hhhhhhhhhhhh.....eeeee.........hhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....-----...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------GLUTR  PDB: A:84-107    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gpj A    1 MEDLVSVGITHKEAEVEELEKARFESDEAVRDIVESFGLSGSVLLQTSNRVEVYASGARDRAEELGDLIHDDAWVKRGSEAVRHLFRVASGLESMMVGEQEILRQVKKAYDRAARLGTLDEALKIVFRRAINLGKRAREETRISEGAVSIGSAAVELAERELGSLHDKTVLVVGAGEMGKTVAKSLVDRGVRAVLVANRTYERAVELARDLGGEAVRFDELVDHLARSDVVVSATAAPHPVIHVDDVREALRKRDRRSPILIIDIANPRDVEEGVENIEDVEVRTIDDLRVIARENLERRRKEIPKVEKLIEEELSTVEEELEKLKERRLVADVAKSLHEIKDRELERALRRLKT-----VLQDFAEAYTKRLINVLTSAIMELPDEYRRAASRALRRASELNGE 1406
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350    |    -|      370       380       390       400   ||
                                                                                                                                                                                                                                                                                                                                                                                            355   361                                        404|
                                                                                                                                                                                                                                                                                                                                                                                                                                             1406
   Legend:   → Mismatch (orange background)
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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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GPJ)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (HEM1_METKA | Q9UXR8)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0008883    glutamyl-tRNA reductase activity    Catalysis of the reaction: (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = L-glutamyl-tRNA(Glu) + H(+) + NADPH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0006782    protoporphyrinogen IX biosynthetic process    The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
    GO:0033014    tetrapyrrole biosynthetic process    The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

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