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(-) Description

Title :  PORPHOBILINOGEN DEAMINASE FROM ARABIDOPSIS THALIANA
 
Authors :  A. Roberts, R. Gill, R. J. Hussey, P. T. Erskine, J. B. Cooper, S. P. Wood, E. J. T. Chrystal, P. M. Shoolingin-Jordan
Date :  01 Nov 12  (Deposition) - 27 Feb 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Type-Ii Periplasmic Binding Protein Fold, Porphyrin Binding, Tetrapyrrole Biosynthesis, Porphobilinogen (Porphyrin) Binding, Chloroplast, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Roberts, R. Gill, R. J. Hussey, H. Mikolajek, P. T. Erskine, J. B. Cooper, S. P. Wood, E. J. Chrystal, P. M. Shoolingin-Jordan
Insights Into The Mechanism Of Pyrrole Polymerization Catalysed By Porphobilinogen Deaminase: High-Resolution X-Ray Studies Of The Arabidopsis Thaliana Enzyme.
Acta Crystallogr. , Sect. D V. 69 471 2013
PubMed-ID: 23519422  |  Reference-DOI: 10.1107/S0907444912052134

(-) Compounds

Molecule 1 - PORPHOBILINOGEN DEAMINASE, CHLOROPLASTIC
    Chains: A
    EC Number: 2.5.1.61
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: T7
    Gene: AT5G08280, F8L15_10, HEMC
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PBG, HYDROXYMETHYLBILANE SYNTHASE, HMBS, PRE- UROPORPHYRINOGEN SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
118W1Ligand/Ion3-[(5Z)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYLIDENE}-4-(CARBOXYMETHYL)-2-OXO-2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC ACID
2ACT1Ligand/IonACETATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
118W1Ligand/Ion3-[(5Z)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYLIDENE}-4-(CARBOXYMETHYL)-2-OXO-2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC ACID
2ACT1Ligand/IonACETATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
118W2Ligand/Ion3-[(5Z)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYLIDENE}-4-(CARBOXYMETHYL)-2-OXO-2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC ACID
2ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:18 , SER A:20 , LEU A:64 , PHE A:73 , LYS A:94 , ASP A:95 , THR A:138 , ALA A:139 , SER A:140 , ARG A:142 , ARG A:143 , ARG A:161 , GLY A:162 , ASN A:163 , VAL A:164 , ARG A:167 , ALA A:207 , CYS A:254 , HOH A:514 , HOH A:651 , HOH A:782 , HOH A:881BINDING SITE FOR RESIDUE 18W A 401
2AC2SOFTWARELYS A:94 , ARG A:143 , LEU A:181 , ALA A:182 , HOH A:517 , HOH A:728BINDING SITE FOR RESIDUE ACT A 402

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4htga1 A:10-231 automated matches                                                                                                                                                                                            d4htga2 A:232-311 automated matches                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhh....hhhhh......hhhhhhhhhh....eeeee.hhh.......eeeeee.......eeeee....hhhhh....eee..hhhhhhhhhhhh...eee.....hhhhhhhhhhh....eeeeehhhhhhhhhhhhh.ee..............eeeeee..hhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeeeeee....eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4htg A  10 TAIIRIGTRGSPLALAQAYETREKLKKKHPELVEDGAIHIEIIKTTGDKILSQPLADIGGKGLFTKEIDEALINGHIDIAVHSMKDVPTYLPEKTILPCNLPREDVRDAFICLTAATLAELPAGSVVGTASLRRKSQILHKYPALHVEENFRGNVQTRLSKLQGGKVQATLLALAGLKRLSMTENVASILSLDEMLPAVAQGAIGIACRTDDDKMATYLASLNHEETRLAISCERAFLETLDGSCRTPIAGYASKDEEGNCIFRGLVASPDGTKVLETSRKGPYVYEDMVKMGKDAGQELLS 311
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309
   Legend:   → Mismatch (orange background)
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 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1gtk PORPHOBILINOGEN DEAMINASE FROM E. COLI
1pda PORPHOBILINOGEN DEAMINASE FROM E. COLI
3ecr PORPHOBILINOGEN DEAMINASE FROM H. SAPIENS
3eq1 PORPHOBILINOGEN DEAMINASE FROM H. SAPIENS