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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS MEGATERIUM PORPHOBILINOGEN DEAMINASE
 
Authors :  N. Azim, E. Deery, M. J. Warren, P. Erskine, J. B. Cooper, A. Coker, S. P. W M. Akhtar
Date :  06 Sep 13  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  A
Keywords :  Tetrapyrrole Biosynthesis, Porphobilinogen Deaminase, Dipyrromethane Cofactor, Three-Domain Fold, Domains 1 And 2 Resemble The Fold Of Type Ii Periplasmic Binding Proteins, Pyrrole Polymerisation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Azim, E. Deery, M. J. Warren, B. A. Wolfenden, P. Erskine, J. B. Cooper, A. Coker, S. P. Wood, M. Akhtar
Structural Evidence For The Partially Oxidized Dipyrromethene And Dipyrromethanone Forms Of The Cofactor O Porphobilinogen Deaminase: Structures Of The Bacillus Megaterium Enzyme At Near-Atomic Resolution.
Acta Crystallogr. , Sect. D V. 70 744 2014
PubMed-ID: 24598743  |  Reference-DOI: 10.1107/S139900471303294X

(-) Compounds

Molecule 1 - PORPHOBILINOGEN DEAMINASE
    Chains: A
    EC Number: 2.5.1.61
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PORPHOBILINOGEN DEAMINASE
    Gene: HEMC
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Synonym: PBG, HYDROXYMETHYLBILANE SYNTHASE, PRE-UROPORPHYRINOGEN SYNTHASE

 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
129P1Ligand/Ion3-[(5S)-5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-2-OXO-2,5-DIHYDRO-1H-PYRROL-3-YL]PROPANOIC ACID
2ACY1Ligand/IonACETIC ACID
3DPM1Ligand/Ion3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:79 , LYS A:81 , ASP A:82 , THR A:125 , SER A:126 , SER A:127 , ARG A:129 , ARG A:130 , ARG A:153 , ALA A:168 , ALA A:194 , GLN A:197 , GLY A:198 , CYS A:241 , HOH A:506 , HOH A:544 , HOH A:559 , HOH A:565BINDING SITE FOR RESIDUE DPM A 401
2AC2SOFTWAREARG A:9 , SER A:11 , LEU A:13 , LYS A:81 , ASP A:82 , THR A:125 , SER A:126 , SER A:127 , ARG A:129 , ARG A:130 , ARG A:147 , GLY A:148 , ASN A:149 , ILE A:150 , ARG A:153 , ALA A:194 , CYS A:241 , HOH A:618 , HOH A:801BINDING SITE FOR RESIDUE 29P A 402
3AC3SOFTWAREPHE A:34 , GLU A:35 , ILE A:36 , ARG A:303 , HOH A:790BINDING SITE FOR RESIDUE ACY A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MLV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MLV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4mlva1 A:-1-218 automated matches                                                                                                                                                                     d4mlva2 A:219-309 automated matches                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhh....eeeee.hhh.......eeeee........eeeee....hhhhh...eeee..hhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeeehhhhhhh........ee..............eeeeee..hhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeeeeee.....eeeeeeee......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mlv A  -1 SHMRKIIVGSRRSKLALTQTKWVIEQLKKQGLPFEFEIKEMVKEIEQAMLDKEIDMAVHSMKDMPAVLPEGLTIGCIPLREDHRDALISKNGERFEELPSGAVIGTSSLRRGAQLLSMRSDIEIKWIRGNIDTRLEKLKNEDYDAIILAAAGLSRMGWSKDTVTQYLEPEISVPAVGQGALAIECRENDHELLSLLQALNHDETARAVRAERVFLKEMEGGCQVPIAGYGRILDGGNIELTSLVASPDGKTIYKEHITGKDPIAIGSEAAERLTSQGAKLLIDRVKEELD 309
                                     8        18        28        38||      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
                                                                   39|                                                                                                                                                                                                                                                        
                                                                    61
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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  (2, 2)

Asymmetric/Biological 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 4MLV)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        Q8GCA8_BACME | Q8GCA8: 4mlq

(-) Related Entries Specified in the PDB File

1pda STRUCTURE OF ESCHERICHIA COLI PORPHOBILINOGEN DEAMINASE
4htg STRUCTURE OF ARABIDOPSIS THALIANA PORPHOBILINOGEN DEAMINASE