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(-) Description

Title :  CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES MALYL-COA LYASE IN COMPLEX WITH MAGNESIUM, GLYOXYLATE, AND PROPIONYL-COA
 
Authors :  J. Zarzycki, C. A. Kerfeld
Date :  18 Jun 13  (Deposition) - 04 Dec 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zarzycki, C. A. Kerfeld
The Crystal Structures Of The Tri-Functional Chloroflexus Aurantiacus And Bi-Functional Rhodobacter Sphaeroides Malyl-Coa Lyases And Comparison With Cite-Like Superfamily Enzymes And Malate Synthases.
Bmc Struct. Biol. V. 13 28 2013
PubMed-ID: 24206647  |  Reference-DOI: 10.1186/1472-6807-13-28

(-) Compounds

Molecule 1 - MALYL-COA LYASE
    Chains: A, B, C, D, E, F
    EC Number: 4.1.3.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MCL1, RHOS4_03500, RSP_1771
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
    Synonym: (3S)-MALYL-COA/BETA-METHYLMALYL-COA LYASE, L-MALYL-COA/BETA- METHYLMALYL-COA LYASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
11VU1Ligand/IonPROPIONYL COENZYME A
2CL4Ligand/IonCHLORIDE ION
3GLV2Ligand/IonGLYOXYLIC ACID
4MG6Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:141 , ASP A:168 , HOH A:501 , HOH A:519 , HOH A:546 , HOH A:602BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREGLY A:165 , ALA A:166 , ALA A:167 , ASP A:168 , HOH A:501BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREASP A:299 , PHE B:19 , GLY B:20 , ARG B:24 , LYS B:30 , MET B:31 , ARG B:76 , ALA B:167 , ILE B:180 , ILE B:251 , HIS B:252 , PRO B:253 , GLV B:402 , HOH B:510 , HOH B:661 , HOH B:691BINDING SITE FOR RESIDUE 1VU B 401
04AC4SOFTWAREARG B:76 , GLU B:141 , GLY B:165 , ALA B:166 , ALA B:167 , ASP B:168 , PRO B:223 , 1VU B:401 , MG B:403 , HOH B:510BINDING SITE FOR RESIDUE GLV B 402
05AC5SOFTWAREASP B:45 , GLU B:141 , ASP B:168 , GLV B:402 , HOH B:510 , HOH B:724BINDING SITE FOR RESIDUE MG B 403
06AC6SOFTWAREASP C:45 , GLU C:141 , ASP C:168 , HOH C:502 , HOH C:503 , HOH C:507 , HOH C:763BINDING SITE FOR RESIDUE MG C 401
07AC7SOFTWAREGLY C:165 , ALA C:166 , ALA C:167 , ASP C:168 , HOH C:502 , HOH C:627BINDING SITE FOR RESIDUE CL C 402
08AC8SOFTWAREARG D:76 , GLU D:141 , GLY D:165 , ALA D:166 , ALA D:167 , ASP D:168 , PRO D:223 , TRP D:249 , MG D:402 , HOH D:501BINDING SITE FOR RESIDUE GLV D 401
09AC9SOFTWAREGLU D:141 , ASP D:168 , GLV D:401 , HOH D:501 , HOH D:733BINDING SITE FOR RESIDUE MG D 402
10BC1SOFTWAREASP E:45 , GLU E:141 , ASP E:168 , HOH E:501 , HOH E:513 , HOH E:724 , HOH E:757BINDING SITE FOR RESIDUE MG E 401
11BC2SOFTWAREGLY E:165 , ALA E:166 , ALA E:167 , ASP E:168 , PRO E:223 , HOH E:724BINDING SITE FOR RESIDUE CL E 402
12BC3SOFTWAREASP F:45 , GLU F:141 , ASP F:168 , HOH F:503 , HOH F:506 , HOH F:526 , HOH F:747BINDING SITE FOR RESIDUE MG F 401
13BC4SOFTWAREGLY F:165 , ALA F:166 , ALA F:167 , ASP F:168 , PRO F:223 , HOH F:747BINDING SITE FOR RESIDUE CL F 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L9Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L9Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4L9Y)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh...eee...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee..eeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9y A   2 SFRLQPAPPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEVIVRQAEM 315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee..hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l9y B   2 SFRLQPAPPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIHPKQVALANEVFTP 265
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    


Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..hhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9y C   2 SFRLQPAPPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEVIVRQAEMIS 317
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311      


Chain D from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9y D   2 SFRLQPAPPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIHPKQVALANEVFTPS 266
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     


Chain E from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9y E   2 SFRLQPAPPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIHPKQVALANEVFTPS 266
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     


Chain F from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9y F   2 SFRLQPAPPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEVIV 310
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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  (0, 0)

(no "SCOP Domain" information available for 4L9Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L9Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L9Y)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        MCAL_RHOS4 | Q3J5L6: 4l9z

(-) Related Entries Specified in the PDB File

4l7z 4l80 4l9z