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(-) Description

Title :  CRYSTAL STRUCTURE OF A RUBISCO-LIKE PROTEIN FROM GEOBACILLUS KAUSTOPHILUS LIGANDED WITH MG2+ AND 2,3-DIKETOHEXANE 1-PHOSPHATE
 
Authors :  A. A. Fedorov, H. J. Imker, E. V. Fedorov, J. A. Gerlt, S. C. Almo
Date :  30 Dec 06  (Deposition) - 20 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rubisco-Like Protein, "Enolase", Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Imker, A. A. Fedorov, E. V. Fedorov, S. C. Almo, J. A. Gerlt
Mechanistic Diversity In The Rubisco Superfamily: The "Enolase" In The Methionine Salvage Pathway In Geobacillus Kaustophilus.
Biochemistry V. 46 4077 2007
PubMed-ID: 17352497  |  Reference-DOI: 10.1021/BI7000483

(-) Compounds

Molecule 1 - 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE
    Chains: A, B
    EC Number: 5.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MTNW
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 1462
    Synonym: DK- MTP-1-P ENOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
11AE2Ligand/Ion(1Z)-2-HYDROXY-3-OXOHEX-1-EN-1-YL DIHYDROGEN PHOSPHATE
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX A:173 , ASP A:175 , GLU A:176 , 1AE A:901 , HOH A:1189BINDING SITE FOR RESIDUE MG A 911
2AC2SOFTWAREKCX B:173 , ASP B:175 , GLU B:176 , HOH B:1003 , HOH B:1225 , HOH B:1233BINDING SITE FOR RESIDUE MG B 912
3AC3SOFTWAREILE A:145 , LYS A:147 , KCX A:173 , ASP A:175 , GLU A:176 , HIS A:264 , ALA A:336 , GLY A:337 , ALA A:358 , GLY A:359 , GLY A:360 , MG A:911 , HOH A:966 , HOH A:978 , HOH A:1191 , LYS B:98 , HOH B:1235BINDING SITE FOR RESIDUE 1AE A 901
4AC4SOFTWARELYS A:98 , GLY B:337 , ALA B:358 , GLY B:359 , GLY B:360 , GLY B:361 , HOH B:1132 , HOH B:1169 , HOH B:1227 , HOH B:1228 , HOH B:1230BINDING SITE FOR RESIDUE 1AE B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OEM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OEM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OEM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OEM)

(-) Exons   (0, 0)

(no "Exon" information available for 2OEM)

(-) 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:408
 aligned with MTNW_GEOKA | Q5L1E2 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:408
                                    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       321       331       341       351       361       371       381       391       401        
           MTNW_GEOKA     2 SAVMATYLLHDETDIRKKAEGIALGLTIGTWTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPALLVTTFGKLSLDGEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTSELKKQALGGVDLVKDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVFAYGLDVLQALREDEEIAVPIMAHPAFSGAVTPSEFYGVAPSLWLGKLLRLAGADFVLFPSPYGSVALEREQALGIARALTDDQEPFARAFPVPSAGIHPGLVPLIIRDFGLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGVV 409
               SCOP domains d2oema1 A:2-120 automated matches                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhh........hhhhhhhhhhhh.eeeeeee...hhhhhhhhh...eeeeeeeeee.hhh..hhhhhhhhhhhhhhhh..eeeeeee.hhhhhh......hhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh......eee...hhhhh........hhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oem A   2 SAVMATYLLHDETDIRKKAEGIALGLTIGTWTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPALLVTTFGKLSLDGEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTSELKKQALGGVDLVkDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVFAYGLDVLQALREDEEIAVPIMAHPAFSGAVTPSEFYGVAPSLWLGKLLRLAGADFVLFPSPYGSVALEREQALGIARALTDDQEPFARAFPVPSAGIHPGLVPLIIRDFGLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGVV 409
                                    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       321       331       341       351       361       371       381       391       401        
                                                                                                                                                                                                     173-KCX                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:412
 aligned with MTNW_GEOKA | Q5L1E2 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:412
                                    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       321       331       341       351       361       371       381       391       401       411  
           MTNW_GEOKA     2 SAVMATYLLHDETDIRKKAEGIALGLTIGTWTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPALLVTTFGKLSLDGEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTSELKKQALGGVDLVKDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVFAYGLDVLQALREDEEIAVPIMAHPAFSGAVTPSEFYGVAPSLWLGKLLRLAGADFVLFPSPYGSVALEREQALGIARALTDDQEPFARAFPVPSAGIHPGLVPLIIRDFGLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGVVEVEA 413
               SCOP domains d2oemb1 B:2-120 automated matches                                                                                      d2oemb2 B:121-413 automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------RuBisCO_large-2oemB01 B:126-409                                                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------RuBisCO_large-2oemB02 B:126-409                                                                                                                                                                                                                                                             ---- Pfam domains (2)
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhh........hhhhhhhhhhhh.eeeeeeee..hhhhhhhhh...eeeeeeeeee.hhh..hhhhhhhhhhhhhhhh..eeeeeee.hhhhhh......hhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh......eee...hhhhh........hhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh...eeeeehhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oem B   2 SAVMATYLLHDETDIRKKAEGIALGLTIGTWTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPALLVTTFGKLSLDGEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTSELKKQALGGVDLVkDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVFAYGLDVLQALREDEEIAVPIMAHPAFSGAVTPSEFYGVAPSLWLGKLLRLAGADFVLFPSPYGSVALEREQALGIARALTDDQEPFARAFPVPSAGIHPGLVPLIIRDFGLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGVVEVEA 413
                                    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       321       331       341       351       361       371       381       391       401       411  
                                                                                                                                                                                                     173-KCX
   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  (2, 3)

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 2OEM)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RuBisCO_large] (36)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MTNW_GEOKA | Q5L1E2)
molecular function
    GO:0043715    2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity    Catalysis of the reaction: 2,3-diketo-5-methylthiopentyl-1-phosphate = H+ + 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate. 2,3-diketo-5-methylthiopentyl-1-phosphate is also known as DK-MTP-1-P, and 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate as HK-MTPenyl-1-P.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016984    ribulose-bisphosphate carboxylase activity    Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
    GO:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0015977    carbon fixation    A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

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 Related Entries

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        MTNW_GEOKA | Q5L1E2: 2oej 2oek 2oel

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