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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUTATIVE PROLINE RACEMASE FROM BRUCELLA MELITENSIS, NORTHEAST STRUCTURAL GENOMICS TARGET LR31
 
Authors :  F. Forouhar, Y. Chen, R. Xiao, C. K. Ho, L. -C. Ma, B. Cooper, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)
Date :  10 Jun 04  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Keywords :  Structural Genomics, Alpha-Beta Protein That Resembles Double-Beta Barrel, In Each Of Which An Alpha Helix Is Sandwiched, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, A. Kuzin, J. Seetharaman, I. Lee, W. Zhou, M. Abashidze, Y. Chen, W. Yong, H. Janjua, Y. Fang, D. Wang, K. Cunningham, R. Xiao, T. B. Acton, E. Pichersky, D. F. Klessig, C. W. Porter, G. T. Montelione L. Tong
Functional Insights From Structural Genomics.
J. Struct. Funct. Genom. V. 8 37 2007
PubMed-ID: 17588214  |  Reference-DOI: 10.1007/S10969-007-9018-3

(-) Compounds

Molecule 1 - PROLINE RACEMASE
    Chains: A, B
    EC Number: 5.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21(BL21)
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 224914
    Strain: 16M

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (1x): A 
Biological Unit 4 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 40)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1TM0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TM0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:54 -Pro A:55
2Glu A:111 -Pro A:112
3Lys B:54 -Pro B:55
4Glu B:111 -Pro B:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TM0)

(-) Exons   (0, 0)

(no "Exon" information available for 1TM0)

(-) 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:311
 aligned with Y1586_BRUME | Q8YFD6 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:332
                                    10        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  
          Y1586_BRUME     1 MRSTKVIHIVGCHAEGEVGDVIVGGVAPPPGETVWEQSRFIANDETLRNFVLNKPRGGVFRHVNLLVPPKDPRAQMGFIIMEPADTPPMSGSNSICVSTVLLDSGIIAMQEPVTHMVLEAPGGIIEVEAECRNGKAERISVRNVPSFADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQIGMKIEPGQARELAEIGVKITKAANEQLGFRHPERDWRHISFCQITEPVTREGDVLTGVNTVAIRPAKFDRSPTGTGCSARMAVLHAKGQMKAGERFIGKSVLGTEFHCRLDKVLELGGKPAISPIISGRAWVTGTSQLMLDPSDPFPHGY 332
               SCOP domains d1tm0a_ A: Proline racemase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1tm0A01 A:2-143,A:311-332 Diaminopimelate Epimerase; Chain A, domain 1                                                                        1tm0A02 A:144-310 Diaminopimelate Epimer   ase; Chain A, doma      in 1                                                                                                1tm0A01                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..ee.eeeee........hhhhhhhhhhhhhhhhhhhhh.........eeeee........eeee..........hhhhhhhhhhhhhhh........eeeeeee....eeeeeeee....eeeeeee....ee....eeee.....eeeeeeee...eeeeee.hhh.---hhhhhhhhhhhhhhhhh.------............eeeee...ee...eeee.ee.----------.hhhhhhhhhhhhhhh.......eeee...--..eeeeeeeeeee..eeeeeeeeee.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tm0 A   1 mRSTKVIHIVGCHAEGEVGDVIVGGVAPPPGETVWEQSRFIANDETLRNFVLNKPRGGVFRHVNLLVPPKDPRAQmGFIImEPADTPPmSGSNSICVSTVLLDSGIIAmQEPVTHmVLEAPGGIIEVEAECRNGKAERISVRNVPSFADRLDAPLDVTGLGTImVDTAYGGDSFVIVDAAQIG---EPGQARELAEIGVKITKA------FRHPERDWRHISFCQITEPVTREGDVLTGVNTV----------PTGTGCSARmAVLHAKGQmKAGERFIGKSV--TEFHCRLDKVLELGGKPAISPIISGRAWVTGTSQLmLDPSDPFPHGY 332
                            |       10        20        30        40        50        60        70     |  80|       90       100       110     | 120       130       140       150       160   |   170       180  |   |190       200   |     -|      220       230       240  |      -   |   260  |    270 |     280  |  | 290       300       310       320|      330  
                            |                                                                         76-MSE|      89-MSE             109-MSE  |                                             164-MSE            183 187              204    211                             243        254      263-MSE  272-MSE    283  |                                321-MSE       
                            1-MSE                                                                          81-MSE                            116-MSE                                                                                                                                                                   286                                              


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with Y1586_BRUME | Q8YFD6 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:332
                                    10        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  
          Y1586_BRUME     1 MRSTKVIHIVGCHAEGEVGDVIVGGVAPPPGETVWEQSRFIANDETLRNFVLNKPRGGVFRHVNLLVPPKDPRAQMGFIIMEPADTPPMSGSNSICVSTVLLDSGIIAMQEPVTHMVLEAPGGIIEVEAECRNGKAERISVRNVPSFADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQIGMKIEPGQARELAEIGVKITKAANEQLGFRHPERDWRHISFCQITEPVTREGDVLTGVNTVAIRPAKFDRSPTGTGCSARMAVLHAKGQMKAGERFIGKSVLGTEFHCRLDKVLELGGKPAISPIISGRAWVTGTSQLMLDPSDPFPHGY 332
               SCOP domains d1tm0b_ B: Proline racemase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1tm0B01 B:2-143,B:311-332 Diaminopimelate Epimerase; Chain A, domain 1                                                                        1tm0B02 B:144-310 Diaminopimelate Epimer   ase; Chain A, doma      in 1                                                                                                1tm0B01                CATH domains
           Pfam domains (1) --------Pro_racemase-1tm0B01 B:9-332                                                                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --------Pro_racemase-1tm0B02 B:9-332                                                                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .....eeeeeeeee..ee.eeeee........hhhhhhhhhhhhhhhhhhhhh.........eeeee........eeee..........hhhhhhhhhhhhhhh........eeeeeee....eeeeeeee....eeeeeee....ee....eeee.....eeeeeeee...eeeeee.hhh.---hhhhhhhhhhhhhhhhh.------............eeeee...ee...eeee....----------..hhhhhhhhhhhh.........eeee...--...eeeeeeeee....eeeeeeeee.eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tm0 B   1 mRSTKVIHIVGCHAEGEVGDVIVGGVAPPPGETVWEQSRFIANDETLRNFVLNKPRGGVFRHVNLLVPPKDPRAQmGFIImEPADTPPmSGSNSICVSTVLLDSGIIAmQEPVTHmVLEAPGGIIEVEAECRNGKAERISVRNVPSFADRLDAPLDVTGLGTImVDTAYGGDSFVIVDAAQIG---EPGQARELAEIGVKITKA------FRHPERDWRHISFCQITEPVTREGDVLTGVNTV----------PTGTGCSARmAVLHAKGQmKAGERFIGKSV--TEFHCRLDKVLELGGKPAISPIISGRAWVTGTSQLmLDPSDPFPHGY 332
                            |       10        20        30        40        50        60        70     |  80|       90       100       110     | 120       130       140       150       160   |   170       180  |   |190       200   |     -|      220       230       240  |      -   |   260  |    270 |     280  |  | 290       300       310       320|      330  
                            1-MSE                                                                     76-MSE|      89-MSE             109-MSE  |                                             164-MSE            183 187              204    211                             243        254      263-MSE  272-MSE    283  |                                321-MSE       
                                                                                                           81-MSE                            116-MSE                                                                                                                                                                   286
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DAP_epimerase (14)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Y1586_BRUME | Q8YFD6)
molecular function
    GO:0047580    4-hydroxyproline epimerase activity    Catalysis of the reaction: trans-4-hydroxy-L-proline = cis-4-hydroxy-D-proline.
    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.

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lr31