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(-) Description

Title :  CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME-LIKE PROTEIN FROM RUBROBACTER XYLANOPHILUS DSM 9941
 
Authors :  S. Eswaramoorthy, M. Madegowda, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  26 Jul 07  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Enolase, Mg Ion, 9367A, Psi-2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, M. Madegowda, S. K. Burley, S. Swaminathan
Crystal Structure Of Mandelate Racemase/Muconate Lactonizing Enzyme-Like Protein From Rubrobacter Xylanophilus Dsm 9941.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME- LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RXYL_0547
    Organism Scientific: RUBROBACTER XYLANOPHILUS DSM 9941
    Organism Taxid: 266117
    Strain: DSM 9941, NBRC 16129

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 64)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE64Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:167 , ASP A:214 , GLU A:240 , GLU A:266BINDING SITE FOR RESIDUE MG A 409
2AC2SOFTWARELYS B:167 , ASP B:214 , GLU B:240 , GLU B:266 , HIS B:316BINDING SITE FOR RESIDUE MG B 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 2QQ6)

(-) 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:394
 aligned with Q1AYK7_RUBXD | Q1AYK7 from UniProtKB/TrEMBL  Length:400

    Alignment length:397
                                    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       
         Q1AYK7_RUBXD     2 SAPRITRVETAAIRAVGPSVLVRVWAGDEHGLGECYPSAPAAGIHHIVMNMEEQLLGEDPRDVERLYEKMRRWNIFTGGQAGAVITALSGIETALWDLAGKLQGVPVYRLLGGAFRRRVRLYADCNAGTVDAAAHHIEGGLFEEGSNEEYIAVAREAVERGFDAIKLDVDDITGPLHRDFWNGAISPREHEAMVARVAAVREAVGPEVEVAIDMHGRFDIPSSIRFARAMEPFGLLWLEEPTPPENLDALAEVRRSTSTPICAGENVYTRFDFRELFAKRAVDYVMPDVAKCGGLAEAKRIANLAELDYIPFAPHNVSSPVGTVAAAHVCAAVSNFAVLEWHAIDMPHWEDFVRYPGGPVIREGHIELTEEPGLGLELDEEAAFEHRHEKGGVPFFG 398
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----2qq6A01 A:7 -105,A:373-390 Enolase-like, N-terminal domain                                         2qq6A02 A:106-372 Enolase superfamily                                                                                                                                                                                                                                      2qq6A01             ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...-.eeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee....ee.....eee......hhhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh......eee......hhhhhh.......ee..eee....hhhhh..hhhhhhh....--...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qq6 A   2 SAPRITRVETAAIRAV-PSVLVRVWAGDEHGLGECYPSAPAAGIHHIVmNmEEQLLGEDPRDVERLYEKmRRWNIFTGGQAGAVITALSGIETALWDLAGKLQGVPVYRLLGGAFRRRVRLYADCNAGTVDAAAHHIEGGLFEEGSNEEYIAVAREAVERGFDAIKLDVDDITGPLHRDFWNGAISPREHEAmVARVAAVREAVGPEVEVAIDmHGRFDIPSSIRFARAmEPFGLLWLEEPTPPENLDALAEVRRSTSTPICAGENVYTRFDFRELFAKRAVDYVmPDVAKCGGLAEAKRIANLAELDYIPFAPHNVSSPVGTVAAAHVCAAVSNFAVLEWHAIDmPHWEDFVRYPGGPVIREGHIELTEEPGLGLELDEEAAFEHRHE--GVPFFG 398
                                    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        |- |     
                                          17 |                             50-MSE               71-MSE                                                                                                                    194-MSE              215-MSE         231-MSE                                                 287-MSE                                                     347-MSE                                    390  |     
                                            19                               52-MSE                                                                                                                                                                                                                                                                                                                                              393     


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with Q1AYK7_RUBXD | Q1AYK7 from UniProtKB/TrEMBL  Length:400

    Alignment length:397
                                    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       
         Q1AYK7_RUBXD     2 SAPRITRVETAAIRAVGPSVLVRVWAGDEHGLGECYPSAPAAGIHHIVMNMEEQLLGEDPRDVERLYEKMRRWNIFTGGQAGAVITALSGIETALWDLAGKLQGVPVYRLLGGAFRRRVRLYADCNAGTVDAAAHHIEGGLFEEGSNEEYIAVAREAVERGFDAIKLDVDDITGPLHRDFWNGAISPREHEAMVARVAAVREAVGPEVEVAIDMHGRFDIPSSIRFARAMEPFGLLWLEEPTPPENLDALAEVRRSTSTPICAGENVYTRFDFRELFAKRAVDYVMPDVAKCGGLAEAKRIANLAELDYIPFAPHNVSSPVGTVAAAHVCAAVSNFAVLEWHAIDMPHWEDFVRYPGGPVIREGHIELTEEPGLGLELDEEAAFEHRHEKGGVPFFG 398
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----2qq6B01 B:7-105,B:373-391 Enolase-like, N-terminal domain                                          2qq6B02 B:106-372 Enolase superfamily                                                                                                                                                                                                                                      2qq6B01            ------- CATH domains
           Pfam domains (1) ---MR_MLE_N-2qq6B01 B:5-113                                                                                     -----------------------------------------------------------------------------------MR_MLE-2qq6B03 B:197-265                                             ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---MR_MLE_N-2qq6B02 B:5-113                                                                                     -----------------------------------------------------------------------------------MR_MLE-2qq6B04 B:197-265                                             ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeeeeee...eeeeeeeee..eeeeee.....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......eeeeeee.hhhhh..............hhhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh...ee......hhhhhhhhhh.....eee....hhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh......eee.......hhh.ee..........eee....hhhhheehhhhhhhh....-...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qq6 B   2 SAPRITRVETAAIRAVGPSVLVRVWAGDEHGLGECYPSAPAAGIHHIVmNmEEQLLGEDPRDVERLYEKmRRWNIFTGGQAGAVITALSGIETALWDLAGKLQGVPVYRLLGGAFRRRVRLYADCNAGTVDAAAHHIEGGLFEEGSNEEYIAVAREAVERGFDAIKLDVDDITGPLHRDFWNGAISPREHEAmVARVAAVREAVGPEVEVAIDmHGRFDIPSSIRFARAmEPFGLLWLEEPTPPENLDALAEVRRSTSTPICAGENVYTRFDFRELFAKRAVDYVmPDVAKCGGLAEAKRIANLAELDYIPFAPHNVSSPVGTVAAAHVCAAVSNFAVLEWHAIDmPHWEDFVRYPGGPVIREGHIELTEEPGLGLELDEEAAFEHRHEK-GVPFFG 398
                                    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 |     
                                                                           50-MSE               71-MSE                                                                                                                    194-MSE              215-MSE         231-MSE                                                 287-MSE                                                     347-MSE                                     391 |     
                                                                             52-MSE                                                                                                                                                                                                                                                                                                                                              393
   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 2QQ6)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q1AYK7_RUBXD | Q1AYK7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009063    cellular amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  2qq6
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