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(-) Description

Title :  CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM POLAROMONAS SP. JS666
 
Authors :  D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  05 Jan 07  (Deposition) - 27 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Nysgxrc, Protein Structure Initiative (Psi) Ii, Psi-2, 9382A, Mandelate Racemase, Enolase Superfamily, Tim Barrel, Structural Genomics, New York Sgx Research Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, V. Sridhar, S. K. Burley, S. Swaminathan
Crystal Structure Of Mandelate Racemase/Muconate Lactonizin Enzyme From Polaromonas Sp. Js666
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME
    Atcc: BAA-500
    Chains: A, B
    EC Number: 5.1.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BPRO_0435
    Organism Scientific: POLAROMONAS SP.
    Organism Taxid: 296591
    Strain: JS666

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 72)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE72Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:254 , PHE A:257 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:405 , HOH A:567BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREALA B:254 , PHE B:257 , HOH B:403 , HOH B:404 , HOH B:405 , HOH B:406 , HOH B:573BINDING SITE FOR RESIDUE CA B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OG9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OG9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OG9)

(-) Exons   (0, 0)

(no "Exon" information available for 2OG9)

(-) 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:363
 aligned with Q12GE3_POLSJ | Q12GE3 from UniProtKB/TrEMBL  Length:383

    Alignment length:375
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378     
         Q12GE3_POLSJ     9 PSDRITWVRISSCYLPLATPISDAKVLTGRQKPMTEIAILFAEIETAGGHQGLGFSYSKRAGGPGQFAHAREIAPALIGEDPSDIAKLWDKLCWAGASAGRSGLSTQAIGAFDVALWDLKAKRAGLSLAKLLGSYRDSVRCYNTSGGFLHTPIDQLMVNASASIERGIGGIKLKVGQPDGALDIARVTAVRKHLGDAVPLMVDANQQWDRPTAQRMCRIFEPFNLVWIEEPLDAYDHEGHAALALQFDTPIATGEMLTSAAEHGDLIRHRAADYLMPDAPRVGGITPFLKIASLAEHAGLMLAPHFAMELHVHLAAAYPREPWVEHFEWLEPLFNERIEIRDGRMLVPTRPGLGLTLSGQVKAWTREEAQVGTRP 383
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2og9A01 A:11-135,A:36            9-385 Enolase-like, N-terminal domain                                                       2og9A02 A:136-368 Enolase superfamily                                                                                                                                                                                                    2og9A01           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee.....------------..eeeeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....eeeee.........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhh.....eee....hhhhh.....ee..eee............hhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2og9 A  11 PSDRITWVRISSCYLPLATPI------------mTEIAILFAEIETAGGHQGLGFSYSKRAGGPGQFAHAREIAPALIGEDPSDIAKLWDKLCWAGASAGRSGLSTQAIGAFDVALWDLKAKRAGLSLAKLLGSYRDSVRCYNTSGGFLHTPIDQLmVNASASIERGIGGIKLKVGQPDGALDIARVTAVRKHLGDAVPLmVDANQQWDRPTAQRmCRIFEPFNLVWIEEPLDAYDHEGHAALALQFDTPIATGEmLTSAAEHGDLIRHRAADYLmPDAPRVGGITPFLKIASLAEHAGLmLAPHFAmELHVHLAAAYPREPWVEHFEWLEPLFNERIEIRDGRmLVPTRPGLGLTLSGQVKAWTREEAQVGTRP 385
                                    20        30|        -   |    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     
                                               31           44-MSE                                                                                                                    167-MSE                                     211-MSE        226-MSE                                 266-MSE             286-MSE                  311-MSE  |                                  355-MSE                          
                                                                                                                                                                                                                                                                                                                                             318-MSE                                                               


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with Q12GE3_POLSJ | Q12GE3 from UniProtKB/TrEMBL  Length:383

    Alignment length:375
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378     
         Q12GE3_POLSJ     9 PSDRITWVRISSCYLPLATPISDAKVLTGRQKPMTEIAILFAEIETAGGHQGLGFSYSKRAGGPGQFAHAREIAPALIGEDPSDIAKLWDKLCWAGASAGRSGLSTQAIGAFDVALWDLKAKRAGLSLAKLLGSYRDSVRCYNTSGGFLHTPIDQLMVNASASIERGIGGIKLKVGQPDGALDIARVTAVRKHLGDAVPLMVDANQQWDRPTAQRMCRIFEPFNLVWIEEPLDAYDHEGHAALALQFDTPIATGEMLTSAAEHGDLIRHRAADYLMPDAPRVGGITPFLKIASLAEHAGLMLAPHFAMELHVHLAAAYPREPWVEHFEWLEPLFNERIEIRDGRMLVPTRPGLGLTLSGQVKAWTREEAQVGTRP 383
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2og9B01 B:11-135,B:36            9-385 Enolase-like, N-terminal domain                                                       2og9B02 B:136-368 Enolase superfamily                                                                                                                                                                                                    2og9B01           CATH domains
           Pfam domains (1) ---------------------------------MR_MLE_N-2og9B01 B:44-143                                                                           ----------------------------------------------------MR_MLE-2og9B03 B:196-264                                             ------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------MR_MLE_N-2og9B02 B:44-143                                                                           ----------------------------------------------------MR_MLE-2og9B04 B:196-264                                             ------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeeee.....------------..eeeeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....eeeee.........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhh.....eee....hhhhh.....ee..eee............hhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2og9 B  11 PSDRITWVRISSCYLPLATPI------------mTEIAILFAEIETAGGHQGLGFSYSKRAGGPGQFAHAREIAPALIGEDPSDIAKLWDKLCWAGASAGRSGLSTQAIGAFDVALWDLKAKRAGLSLAKLLGSYRDSVRCYNTSGGFLHTPIDQLmVNASASIERGIGGIKLKVGQPDGALDIARVTAVRKHLGDAVPLmVDANQQWDRPTAQRmCRIFEPFNLVWIEEPLDAYDHEGHAALALQFDTPIATGEmLTSAAEHGDLIRHRAADYLmPDAPRVGGITPFLKIASLAEHAGLmLAPHFAmELHVHLAAAYPREPWVEHFEWLEPLFNERIEIRDGRmLVPTRPGLGLTLSGQVKAWTREEAQVGTRP 385
                                    20        30|        -   |    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     
                                               31           44-MSE                                                                                                                    167-MSE                                     211-MSE        226-MSE                                 266-MSE             286-MSE                  311-MSE  |                                  355-MSE                          
                                                                                                                                                                                                                                                                                                                                             318-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  (0, 0)

(no "SCOP Domain" information available for 2OG9)

(-) 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  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q12GE3_POLSJ | Q12GE3)
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:0008867    galactarate dehydratase activity    Catalysis of the reaction: galactarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.
    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.
    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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