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(-) Description

Title :  CRYSTAL STRUCTURE OF FG41MALONATE SEMIALDEHYDE DECARBOXYLASE INHIBITED BY 3-BROMOPROPIOLATE
 
Authors :  Y. Guo, H. Serrano, G. J. Poelarends, W. H. Johnson Jr. , M. L. Hackert, C. P. Whitman
Date :  01 Jul 13  (Deposition) - 24 Jul 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D  (3x)
Biol. Unit 3:  E  (3x)
Keywords :  The Tautomerase Superfamily, Beta-Alpha-Beta-Motif, Malonate Semialdehyde Decarboxylase, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Guo, H. Serrano, G. J. Poelarends, W. H. Johnson, M. L. Hackert, C. P. Whitman
Kinetic, Mutational, And Structural Analysis Of Malonate Semialdehyde Decarboxylase From Coryneform Bacterium Strain Fg41: Mechanistic Implications For The Decarboxylase And Hydratase Activities.
Biochemistry V. 52 4830 2013
PubMed-ID: 23781927  |  Reference-DOI: 10.1021/BI400567A

(-) Compounds

Molecule 1 - FG41 MALONATE SEMIALDEHYDE DECARBOXYLASE
    Chains: A, B, C, D, E
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3B
    Expression System Strain: BL21-GOLD (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEFORM BACTERIUM
    Organism Taxid: 1728
    Strain: FG41

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABC  
Biological Unit 2 (3x):    D 
Biological Unit 3 (3x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1PO415Ligand/IonPHOSPHATE ION
2PR65Ligand/Ion3-CHLORO-3-OXOPROPANOIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1PO49Ligand/IonPHOSPHATE ION
2PR63Ligand/Ion3-CHLORO-3-OXOPROPANOIC ACID
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1PO49Ligand/IonPHOSPHATE ION
2PR63Ligand/Ion3-CHLORO-3-OXOPROPANOIC ACID
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1PO49Ligand/IonPHOSPHATE ION
2PR63Ligand/Ion3-CHLORO-3-OXOPROPANOIC ACID

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:1 , ASP A:37 , THR A:72 , GLN A:73 , TRP A:114 , TYR A:123BINDING SITE FOR RESIDUE PR6 A 201
02AC2SOFTWARELYS A:81 , GLU A:108 , HOH A:331 , HOH A:332 , HOH A:339 , HOH A:353 , HIS B:112 , ASP B:113BINDING SITE FOR RESIDUE PO4 A 202
03AC3SOFTWAREPRO A:111 , HIS A:112 , HOH A:344 , ILE C:78BINDING SITE FOR RESIDUE PO4 A 203
04AC4SOFTWAREHIS A:45 , ASP A:46 , ASP A:49 , HOH A:350 , LEU B:42 , ALA B:44BINDING SITE FOR RESIDUE PO4 A 204
05AC5SOFTWAREPRO B:1 , ASP B:37 , THR B:72 , GLN B:73 , TRP B:114 , TYR B:123BINDING SITE FOR RESIDUE PR6 B 201
06AC6SOFTWAREHIS B:45 , ASP B:46 , ASP B:49 , LEU C:42 , ALA C:44 , HOH C:358BINDING SITE FOR RESIDUE PO4 B 202
07AC7SOFTWAREILE A:78 , PRO B:111 , HIS B:112 , HOH B:328 , HOH B:343 , HOH E:317BINDING SITE FOR RESIDUE PO4 B 203
08AC8SOFTWAREPRO C:1 , ASP C:37 , THR C:72 , GLN C:73 , TRP C:114 , TYR C:123BINDING SITE FOR RESIDUE PR6 C 201
09AC9SOFTWARELYS B:81 , GLU B:108 , HIS C:112 , ASP C:113BINDING SITE FOR RESIDUE PO4 C 202
10BC1SOFTWARELEU A:42 , THR A:43 , ALA A:44 , HIS C:45 , ASP C:46 , ASP C:49 , HOH C:321 , HOH C:348 , HOH C:380BINDING SITE FOR RESIDUE PO4 C 203
11BC2SOFTWAREILE B:78 , PRO C:111 , HIS C:112 , ILE C:130 , HOH C:375BINDING SITE FOR RESIDUE PO4 C 204
12BC3SOFTWAREALA A:110 , HIS A:112 , ASP A:113 , LYS C:81 , GLU C:108 , HOH C:377BINDING SITE FOR RESIDUE PO4 C 205
13BC4SOFTWAREPRO D:1 , ASP D:37 , THR D:72 , GLN D:73 , TRP D:114 , TYR D:123BINDING SITE FOR RESIDUE PR6 D 201
14BC5SOFTWAREILE D:78 , PRO D:111 , HIS D:112 , ILE D:130BINDING SITE FOR RESIDUE PO4 D 202
15BC6SOFTWARELEU D:42 , THR D:43 , ALA D:44 , HIS D:45 , ASP D:46 , ASP D:49 , HOH D:360BINDING SITE FOR RESIDUE PO4 D 203
16BC7SOFTWARELYS D:81 , GLU D:108 , ALA D:110 , HIS D:112 , ASP D:113 , HOH D:308 , HOH D:376 , HOH D:382BINDING SITE FOR RESIDUE PO4 D 204
17BC8SOFTWAREPRO E:1 , ASP E:37 , THR E:72 , GLN E:73 , TRP E:114 , TYR E:123BINDING SITE FOR RESIDUE PR6 E 201
18BC9SOFTWARELEU E:42 , ALA E:44 , HIS E:45 , ASP E:46 , ASP E:49 , HOH E:349BINDING SITE FOR RESIDUE PO4 E 202
19CC1SOFTWAREPRO E:111 , HIS E:112 , ILE E:130BINDING SITE FOR RESIDUE PO4 E 203
20CC2SOFTWARELYS E:81 , GLU E:108 , ALA E:110 , HIS E:112 , ASP E:113 , HOH E:320 , HOH E:348BINDING SITE FOR RESIDUE PO4 E 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LHO)

(-) 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:131
                                                                                                                                                                   
               SCOP domains d4lhoa_ A: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeeee...hhhhhhhhhhhhhhhhh....hhh.eeeeeeeehhh.ee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lho A   1 PLIRIDLTSDRSREQRRAIADAVHDALVEVLAIPARDRFQILTAHDPSDIIAEDAGLGFQRSPSVVIIHVFTQAGRTIETKQRVFAAITESLAPIGVAGSDVFIAITENAPHDWSFGFGSAQYVTGELAIP 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4lhob_ B: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeeee...hhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhh.ee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lho B   1 PLIRIDLTSDRSREQRRAIADAVHDALVEVLAIPARDRFQILTAHDPSDIIAEDAGLGFQRSPSVVIIHVFTQAGRTIETKQRVFAAITESLAPIGVAGSDVFIAITENAPHDWSFGFGSAQYVTGELAIP 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain C from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4lhoc_ C: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeeee...hhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhh.ee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lho C   1 PLIRIDLTSDRSREQRRAIADAVHDALVEVLAIPARDRFQILTAHDPSDIIAEDAGLGFQRSPSVVIIHVFTQAGRTIETKQRVFAAITESLAPIGVAGSDVFIAITENAPHDWSFGFGSAQYVTGELAIP 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain D from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4lhod_ D: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhh...............eeeeeeee...hhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhhh......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lho D   1 PLIRIDLTSDRSREQRRAIADAVHDALVEVLAIPARDRFQILTAHDPSDIIAEDAGLGFQRSPSVVIIHVFTQAGRTIETKQRVFAAITESLAPIGVAGSDVFIAITENAPHDWSFGFGSAQYVTGELAIP 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain E from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4lhoe_ E: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhh...............eeeeeeee...hhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhhh......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lho E   1 PLIRIDLTSDRSREQRRAIADAVHDALVEVLAIPARDRFQILTAHDPSDIIAEDAGLGFQRSPSVVIIHVFTQAGRTIETKQRVFAAITESLAPIGVAGSDVFIAITENAPHDWSFGFGSAQYVTGELAIP 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 5)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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