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(-) Description

Title :  CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING PROTEIN FROM PARACOCCUS DENITRIFICANS PD1222
 
Authors :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New Y Research Center For Structural Genomics (Nysgxrc)
Date :  21 May 10  (Deposition) - 09 Jun 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Structural Genomics, Crystal Structure, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Enolase, Isomerase, Psi-2, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans Pd1222
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME, C-TERMINAL DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: 69934097, PDEN_0244
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 318586
    Strain: PD1222

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3MSE22Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 88)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MSE88Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:197 , GLU A:223 , GLU A:249 , HOH A:418 , HOH A:419 , HOH A:556BINDING SITE FOR RESIDUE CA A 500
2AC2SOFTWAREGLU A:64 , HOH A:495 , HOH A:496 , HOH A:497BINDING SITE FOR RESIDUE CA A 501
3AC3SOFTWAREVAL A:359 , GLU A:361 , HOH A:580BINDING SITE FOR RESIDUE CA A 502
4AC4SOFTWAREASP B:197 , GLU B:223 , GLU B:249 , HOH B:414 , HOH B:415 , HOH B:416BINDING SITE FOR RESIDUE CA B 500
5AC5SOFTWAREGLU B:67 , HOH B:413 , HOH B:471BINDING SITE FOR RESIDUE CA B 501
6AC6SOFTWAREGLU B:64 , HOH B:483 , HOH B:484 , HOH B:488 , HOH B:489BINDING SITE FOR RESIDUE CA B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N4E)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:86 -Pro A:87
2Arg A:333 -Pro A:334
3Gly B:86 -Pro B:87
4Arg B:333 -Pro B:334

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N4E)

(-) Exons   (0, 0)

(no "Exon" information available for 3N4E)

(-) 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:368
 aligned with A1AYL4_PARDP | A1AYL4 from UniProtKB/TrEMBL  Length:383

    Alignment length:374
                             1                                                                                                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
         A1AYL4_PARDP     - -MKIAKVEALSVAMGDGTGWMPTSAFVRITAEDGTVGWGEASPMLGGIASLGVVARDIAPFLEGQEVLDHAVLLDRMMHRLVKLGPEGIATAALAACDIALWDLKGKLLGQPIYKLLGGAWRTRLPCYSSIGGNAARSVDEVVREVARRVEAEQPAAVKIRWDGDRTRCDVDIPGDIAKARAVRELLGPDAVIGFDANNGYSVGGAIRVGRALEDLGYSWFEEPVQHYHVGAMGEVAQRLDITVSAGEQTYTLQALKDLILSGVRMVQPDIVKMGGITGMMQCAALAHAHGVEFVPHQTQPGVGHFANIHVLSTLMHMTKPVELADRWDRGRPVFRNPAEPVDGHFALGDAPGLGIVVDEDELASRATEITVGR 373
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..------.eeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeeee......hhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh..eee......hhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhh.ee.......hhhhhhhhhhhhh.......eee..hhhhhh............eee...........hhhhhhhheeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4e A   2 SLKIAKVEALSVAmG------PTSAFVRITAEDGTVGWGEASPmLGGIASLGVVARDIAPFLEGQEVLDHAVLLDRmmHRLVKLGPEGIATAALAACDIALWDLKGKLLGQPIYKLLGGAWRTRLPCYSSIGGNAARSVDEVVREVARRVEAEQPAAVKIRWDGDRTRCDVDIPGDIAKARAVRELLGPDAVIGFDANNGYSVGGAIRVGRALEDLGYSWFEEPVQHYHVGAmGEVAQRLDITVSAGEQTYTLQALKDLILSGVRmVQPDIVKmGGITGmmQCAALAHAHGVEFVPHQTQPGVGHFANIHVLSTLmHmTKPVELADRWDRGRPVFRNPAEPVDGHFALGDAPGLGIVVDEDELASRATEITVGR 375
                                    11   ||    - |      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    
                                        15-MSE  23                    45-MSE                           78-MSE                                                                                                                                                     234-MSE                          267-MSE 275-MSE ||                                317-MSE                                                      
                                         16                                                             79-MSE                                                                                                                                                                                                   281-MSE                               319-MSE                                                    
                                                                                                                                                                                                                                                                                                                  282-MSE                                                                                         


Chain B from PDB  Type:PROTEIN  Length:367
 aligned with A1AYL4_PARDP | A1AYL4 from UniProtKB/TrEMBL  Length:383

    Alignment length:373
                             1                                                                                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369   
         A1AYL4_PARDP     - -MKIAKVEALSVAMGDGTGWMPTSAFVRITAEDGTVGWGEASPMLGGIASLGVVARDIAPFLEGQEVLDHAVLLDRMMHRLVKLGPEGIATAALAACDIALWDLKGKLLGQPIYKLLGGAWRTRLPCYSSIGGNAARSVDEVVREVARRVEAEQPAAVKIRWDGDRTRCDVDIPGDIAKARAVRELLGPDAVIGFDANNGYSVGGAIRVGRALEDLGYSWFEEPVQHYHVGAMGEVAQRLDITVSAGEQTYTLQALKDLILSGVRMVQPDIVKMGGITGMMQCAALAHAHGVEFVPHQTQPGVGHFANIHVLSTLMHMTKPVELADRWDRGRPVFRNPAEPVDGHFALGDAPGLGIVVDEDELASRATEITVG 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---MR_MLE_N-3n4      eB01 B:5-119                                                                                     ------------------------------------------------------------MR_MLE-3n4eB03 B:180-248                                             ------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---MR_MLE_N-3n4      eB02 B:5-119                                                                                     ------------------------------------------------------------MR_MLE-3n4eB04 B:180-248                                             ------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...eeeeeeeeee..------.eeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeeee......hhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh..eee......hhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhh.ee.......hhhhhhhhhhhhh.......eee..hhhhhh............eee...........hhhhhhhheeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4e B   2 SLKIAKVEALSVAmG------PTSAFVRITAEDGTVGWGEASPmLGGIASLGVVARDIAPFLEGQEVLDHAVLLDRmmHRLVKLGPEGIATAALAACDIALWDLKGKLLGQPIYKLLGGAWRTRLPCYSSIGGNAARSVDEVVREVARRVEAEQPAAVKIRWDGDRTRCDVDIPGDIAKARAVRELLGPDAVIGFDANNGYSVGGAIRVGRALEDLGYSWFEEPVQHYHVGAmGEVAQRLDITVSAGEQTYTLQALKDLILSGVRmVQPDIVKmGGITGmmQCAALAHAHGVEFVPHQTQPGVGHFANIHVLSTLmHmTKPVELADRWDRGRPVFRNPAEPVDGHFALGDAPGLGIVVDEDELASRATEITVG 374
                                    11   ||    - |      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   
                                        15-MSE  23                    45-MSE                           78-MSE                                                                                                                                                     234-MSE                          267-MSE 275-MSE ||                                317-MSE                                                     
                                         16                                                             79-MSE                                                                                                                                                                                                   281-MSE                               319-MSE                                                   
                                                                                                                                                                                                                                                                                                                  282-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 3N4E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N4E)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1AYL4_PARDP | A1AYL4)
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: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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