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(-) Description

Title :  CRYSTAL STRUCTURE OF A MEMBER OF ENOLASE SUPERFAMILY FROM ROSEOVARIUS NUBINHIBENS ISM
 
Authors :  Y. Patskovsky, J. Bonanno, J. M. Sauder, J. M. Gilmore, M. Iizuka, C. Gro T. Gheyi, S. Sojitra, S. R. Wasserman, J. Koss, J. Gerlt, S. K. Burley, S New York Sgx Research Center For Structural Genomics (Nysgx
Date :  20 Jun 07  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Enolase, Racemase, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomics Research Consortium, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, J. Bonanno, J. M. Sauder, J. M. Gilmore, M. Iizuka, C. Groshong, T. Gheyi, S. Sojitra, S. R. Wasserman, J. Koss, J. Gerlt, S. K. Burley, S. C. Almo
Crystal Structure Of A Member Of Enolase Superfamily From Roseovarius Nubinhibens Ism.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: COG4948, ISM_14065
    Organism Scientific: ROSEOVARIUS NUBINHIBENS
    Organism Taxid: 89187
    Strain: ISM

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:97 , HIS A:98 , HOH A:470 , PRO B:59 , HIS B:98BINDING SITE FOR RESIDUE GOL A 377
2AC2SOFTWAREPRO B:201 , ASP B:225 , GLN B:226 , HIS B:229 , TRP B:254 , CYS B:259 , VAL B:285 , GLY B:286 , TRP B:287 , HOH B:442 , HOH B:499BINDING SITE FOR RESIDUE GOL B 377

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QDD)

(-) 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 A3SNF7_ROSNI | A3SNF7 from UniProtKB/TrEMBL  Length:368

    Alignment length:370
                             1                                                                                                                                                                                                                                                                                                                                                                            368 
                             |       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        |-
         A3SNF7_ROSNI     - -MRITRLTVFHLDLPLAKPYWLSGGRLKFDRLDSTYLRIDTDEGVTGWGEGCPWGHSYLPAHGPGLRAGIATLAPHLLGLDPRSLDHVNRVMDLQLPGHSYVKSPIDMACWDILGQVAGLPLWQLLGGEAATPVPINSSISTGTPDQMLGLIAEAAAQGYRTHSAKIGGSDPAQDIARIEAISAGLPDGHRVTFDVNRAWTPAIAVEVLNSVRARDWIEQPCQTLDQCAHVARRVANPIMLDECLHEFSDHLAAWSRGACEGVKIKPNRVGGLTRARQIRDFGVSVGWQMHIEDVGGTALADTAALHLAASTPEANRLASWLGHAHLADDPIPGQGARNRDGLATPPSAPGLGVIPDPEALGRPVASYD-   -
               SCOP domains d2qdda1 A:0-127 automate  d matches                                                                                             d2qdda2 A:128-369 automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------2qddA02 A:119-356 Enolase superfamily                                                                                                                                                                                                         ------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeeee...--.eeeeeeeeeeeeee....eeeeee..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh.......ee.eeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhh......eee....hhhhhhhhhh.....eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh..........hhhhhh...............ee............hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdd A   0 SLRITRLTVFHLDLPLAKPYWLSG--LKFDRLDSTYLRIDTDEGVTGWGEGCPWGHSYLPAHGPGLRAGIATLAPHLLGLDPRSLDHVNRVMDLQLPGHSYVKSPIDMACWDILGQVAGLPLWQLLGGEAATPVPINSSISTGTPDQMLGLIAEAAAQGYRTHSAKIGGSDPAQDIARIEAISAGLPDGHRVTFDVNRAWTPAIAVEVLNSVRARDWIEQPCQTLDQCAHVARRVANPIMLDECLHEFSDHLAAWSRGACEGVKIKPNRVGGLTRARQIRDFGVSVGWQMHIEDVGGTALADTAALHLAASTPEANRLASWLGHAHLADDPIPGQGARNRDGLATPPSAPGLGVIPDPEALGRPVASYDE 369
                                     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
                                                  23 26                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with A3SNF7_ROSNI | A3SNF7 from UniProtKB/TrEMBL  Length:368

    Alignment length:377
                             1                                                                                                                                                                                                                                                                                                                                                                            368        
                             |       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        |-       
         A3SNF7_ROSNI     - -MRITRLTVFHLDLPLAKPYWLSGGRLKFDRLDSTYLRIDTDEGVTGWGEGCPWGHSYLPAHGPGLRAGIATLAPHLLGLDPRSLDHVNRVMDLQLPGHSYVKSPIDMACWDILGQVAGLPLWQLLGGEAATPVPINSSISTGTPDQMLGLIAEAAAQGYRTHSAKIGGSDPAQDIARIEAISAGLPDGHRVTFDVNRAWTPAIAVEVLNSVRARDWIEQPCQTLDQCAHVARRVANPIMLDECLHEFSDHLAAWSRGACEGVKIKPNRVGGLTRARQIRDFGVSVGWQMHIEDVGGTALADTAALHLAASTPEANRLASWLGHAHLADDPIPGQGARNRDGLATPPSAPGLGVIPDPEALGRPVASYD--------   -
               SCOP domains d2qddb1 B:0-127 aut         omated matches                                                                                      d2qddb2 B:128-376 automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------2qddB02 B:119-352 Enolase superfamily                                                                                                                                                                                                     ------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee....---------..eeeeeeeeeee....eeeeee..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh.......ee.eeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhh......eee....hhhhhhhhhh.....eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh.hhhhh....hhhhhh...............ee............hhhhhh...eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdd B   0 SLRITRLTVFHLDLPLAKP---------FDRLDSTYLRIDTDEGVTGWGEGCPWGHSYLPAHGPGLRAGIATLAPHLLGLDPRSLDHVNRVMDLQLPGHSYVKSPIDMACWDILGQVAGLPLWQLLGGEAATPVPINSSISTGTPDQMLGLIAEAAAQGYRTHSAKIGGSDPAQDIARIEAISAGLPDGHRVTFDVNRAWTPAIAVEVLNSVRARDWIEQPCQTLDQCAHVARRVANPIMLDECLHEFSDHLAAWSRGACEGVKIKPNRVGGLTRARQIRDFGVSVGWQMHIEDVGGTALADTAALHLAASTPEANRLASWLGHAHLADDPIPGQGARNRDGLATPPSAPGLGVIPDPEALGRPVASYDEGHHHHHH 376
                                     9        |-        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       
                                             18        28
   Legend:   → Mismatch (orange background)
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    → 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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QDD)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A3SNF7_ROSNI | A3SNF7)
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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        A3SNF7_ROSNI | A3SNF7: 3fvd

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