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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-METHYLCITRATE DEHYDRATASE
 
Authors :  K. R. Rajashankar, R. Kniewel, V. Solorzano, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  06 Apr 04  (Deposition) - 27 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Propionate Catabolism, 2-Methylcitric Acid Cycle Structural Genomics Target, T819, Nysgxrc, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R. Rajashankar, R. Kniewel, V. Solorzano, C. D. Lima
Crystal Structure Of 2-Methylcitrate Dehydratase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-METHYLCITRATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.79
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET T7
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRPD, B0334
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: B834, DE3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric/Biological Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1SZQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:214 -Pro A:215
2Ala B:214 -Pro B:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SZQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1SZQ)

(-) 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:473
 aligned with PRPD_ECOLI | P77243 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:473
                                    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       410       420       430       440       450       460       470       480   
           PRPD_ECOLI    11 EFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVASTAVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGRLTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDLYVI 483
               SCOP domains d1szqa_ A: 2-methylcitrate dehydratase PrpD                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1szqA02 A:285-426 2-methylcitrate dehydratase PrpD                                                                                            --------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..............ee......eehhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhh............hhhhhhh...........hhhhhhhhhhhhhhhhhh..hhh.eeeeeeeehhhhhhhhh......hhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhh.......eeeeeee........eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1szq A  11 EFDREIVDIVDYVmNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAmIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNAVASGKAPLTmKQVLTAmIKAHEIQGCIALENSFNRVGLDHVLLVKVASTAVVAEmLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALmAKTGEmGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVmENVLFKISFPAEFHSQTAVEAAmTLYEQmQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYmVAIPLLFGRLTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQmPVNEYLDLYVI 483
                                    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       410       420       430       440       450       460       470 |     480   
                                        24-MSE                                                                 95-MSE                                       141-MSE  |                                   186-MSE                                             238-MSE |                               278-MSE                301-MSE |                                         351-MSE                                                                                                                  472-MSE       
                                                                                                                                                                   148-MSE                                                                                         244-MSE                                                        307-MSE                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:473
 aligned with PRPD_ECOLI | P77243 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:473
                                    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       410       420       430       440       450       460       470       480   
           PRPD_ECOLI    11 EFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVASTAVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGRLTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDLYVI 483
               SCOP domains d1szqb_ B: 2-methylcitrate dehydratase PrpD                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1szqB02 B:285-426 2-methylcitrate dehydratase PrpD                                                                                            --------------------------------------------------------- CATH domains
           Pfam domains (1) --MmgE_PrpD-1szqB01 B:13-475                                                                                                                                                                                                                                                                                                                                                                                                                                                     -------- Pfam domains (1)
           Pfam domains (2) --MmgE_PrpD-1szqB02 B:13-475                                                                                                                                                                                                                                                                                                                                                                                                                                                     -------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..............ee......eehhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhh............hhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhh.eeeeeeeehhhhhhhh.......hhhhhh...hhhhhhhhhh..............hhhhhhhhh.eeeeehhhhhhhhhh.......eeeeeee........eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1szq B  11 EFDREIVDIVDYVmNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAmIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNAVASGKAPLTmKQVLTAmIKAHEIQGCIALENSFNRVGLDHVLLVKVASTAVVAEmLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALmAKTGEmGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVmENVLFKISFPAEFHSQTAVEAAmTLYEQmQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYmVAIPLLFGRLTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQmPVNEYLDLYVI 483
                                    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       410       420       430       440       450       460       470 |     480   
                                        24-MSE                                                                 95-MSE                                       141-MSE  |                                   186-MSE                                             238-MSE |                               278-MSE                301-MSE |                                         351-MSE                                                                                                                  472-MSE       
                                                                                                                                                                   148-MSE                                                                                         244-MSE                                                        307-MSE
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MmgE_PrpD] (1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRPD_ECOLI | P77243)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0047547    2-methylcitrate dehydratase activity    Catalysis of the reaction: (2S,3S)-2-methylcitrate = cis-2-methylaconitate + H(2)O.
    GO:0003994    aconitate hydratase activity    Catalysis of the reaction: citrate = isocitrate. The reaction occurs in two steps: (1) citrate = cis-aconitate + H2O, (2) cis-aconitate + H2O = isocitrate. This reaction is the interconversion of citrate and isocitrate via the labile, enzyme-bound intermediate cis-aconitate. Water is removed from one part of the citrate molecule and added back to a different atom to form isocitrate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0019629    propionate catabolic process, 2-methylcitrate cycle    The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.
    GO:0019679    propionate metabolic process, methylcitrate cycle    The chemical reactions and pathways involving propionate that occur in the methylcitrate cycle.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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