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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE GLUCARATE DEHYDRATASE FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 COMPLEXED WITH MAGNESIUM
 
Authors :  Y. Patskovsky, R. Toro, M. Rutter, J. M. Sauder, J. A. Gerlt, S. C. Almo, S. K. Burley, New York Structural Genomix Research Consortium (Nysgxrc), New York Sgx Research Center For Structural Genom (Nysgxrc)
Date :  10 Jun 10  (Deposition) - 23 Jun 10  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Structural Genomics, Protein Structure Initiative, Psi, Nysgrc, New York Structural Genomics Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, M. Rutter, J. M. Sauder, J. A. Gerlt, S. K. Burley, S. C. Almo
Crystal Structure Of Glucarate Dehydratase From Chromohalobacter Salexigens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUCARATE DEHYDRATASE
    Atcc: BAA-138, NCIMB 13768
    Chains: A, B
    EC Number: 4.2.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: CSAL_2481
    Organism Scientific: CHROMOHALOBACTER SALEXIGENS
    Organism Taxid: 290398
    Strain: DSM 3043

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:22 , HIS A:27 , THR A:98 , TYR A:146 , PHE A:148 , LYS A:203 , ASN A:337 , HIS A:364 , ARG A:417 , HOH A:481 , HOH A:651 , HOH A:652BINDING SITE FOR RESIDUE SO4 A 449
2AC2SOFTWAREARG A:372 , LYS A:401 , ARG B:208BINDING SITE FOR RESIDUE SO4 A 450
3AC3SOFTWAREASP A:231 , ASN A:233 , GLU A:256 , ASP A:257 , ASN A:285BINDING SITE FOR RESIDUE MG A 451
4AC4SOFTWAREARG A:194 , TYR A:195 , ASP A:369 , GLN A:379 , ILE A:380 , HOH A:598BINDING SITE FOR RESIDUE GOL A 452
5AC5SOFTWAREASN B:22 , HIS B:27 , THR B:98 , TYR B:146 , PHE B:148 , LYS B:203 , ASN B:337 , HIS B:364 , ARG B:417 , HOH B:452 , HOH B:454 , HOH B:611BINDING SITE FOR RESIDUE SO4 B 449
6AC6SOFTWAREARG B:372 , LYS B:401 , HOH B:535BINDING SITE FOR RESIDUE SO4 B 450
7AC7SOFTWAREASP B:231 , ASN B:233 , GLU B:256 , ASP B:257 , ASN B:285BINDING SITE FOR RESIDUE MG B 451

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NFU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NFU)

(-) Sequences/Alignments

Asymmetric/Biological 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:441
 aligned with Q1QUN0_CHRSD | Q1QUN0 from UniProtKB/TrEMBL  Length:441

    Alignment length:441
                                    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       340       350       360       370       380       390       400       410       420       430       440 
         Q1QUN0_CHRSD     1 MFPKITKMNVVPVAGEDGFLLNLSGGHEPWFIRCVLVLEDESGNRGVGEIPSSEGILNGLEKCRSLVEGARVNEVKQVLSRARGLLAQGGPEERGRQTFDLRVAVHVITAIESALFDLFGQALGMPVADLLGQYGRQRDEVEALGYLFLLGDPDKTDLPYPRVADPVDAWDEVRYREAMTPEAVANLARAAYDRYGFKDFKLKGGVLRGEEEADCIRALHEAFPEARLALDPNGAWKLDEAVRVLEPIKHLLSYAEDPCGQEGGFSGRETMAEFKKRTGLPTATNMIATDYKQLQYAVQLNSVDIPLADCHFWTMQGAVAVGELCNEWGMTWGSHSNNHFDISLAMMTHVAAACPGEITAIDTHWIWQDGQRITREPFQIRDGKLTVPKTPGLGIELDDDKLMEAHETYKRLDVTQRNDAMAMQYLIPGWEFDPKRPALVR 441
               SCOP domains d3nfua1 A:1-132 automated matches                                                                                                   d3nfua2 A:133-441 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...eee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhh.........eee..eee.ee.hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh.eee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..........hhhhhh..........ee..eee...........hhhhhhhhhhhhhhhh......hhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfu A   1 LFPKITKMNVVPVAGEDGFLLNLSGGHEPWFIRCVLVLEDESGNRGVGEIPSSEGILNGLEKCRSLVEGARVNEVKQVLSRARGLLAQGGPEERGRQTFDLRVAVHVITAIESALFDLFGQALGMPVADLLGQYGRQRDEVEALGYLFLLGDPDKTDLPYPRVADPVDAWDEVRYREAMTPEAVANLARAAYDRYGFKDFKLKGGVLRGEEEADCIRALHEAFPEARLALDPNGAWKLDEAVRVLEPIKHLLSYAEDPCGQEGGFSGRETMAEFKKRTGLPTATNMIATDYKQLQYAVQLNSVDIPLADCHFWTMQGAVAVGELCNEWGMTWGSHSNNHFDISLAMMTHVAAACPGEITAIDTHWIWQDGQRITREPFQIRDGKLTVPKTPGLGIELDDDKLMEAHETYKRLDVTQRNDAMAMQYLIPGWEFDPKRPALVE 441
                                    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       340       350       360       370       380       390       400       410       420       430       440 


Chain B from PDB  Type:PROTEIN  Length:441
 aligned with Q1QUN0_CHRSD | Q1QUN0 from UniProtKB/TrEMBL  Length:441

    Alignment length:441
                                    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       340       350       360       370       380       390       400       410       420       430       440 
         Q1QUN0_CHRSD     1 MFPKITKMNVVPVAGEDGFLLNLSGGHEPWFIRCVLVLEDESGNRGVGEIPSSEGILNGLEKCRSLVEGARVNEVKQVLSRARGLLAQGGPEERGRQTFDLRVAVHVITAIESALFDLFGQALGMPVADLLGQYGRQRDEVEALGYLFLLGDPDKTDLPYPRVADPVDAWDEVRYREAMTPEAVANLARAAYDRYGFKDFKLKGGVLRGEEEADCIRALHEAFPEARLALDPNGAWKLDEAVRVLEPIKHLLSYAEDPCGQEGGFSGRETMAEFKKRTGLPTATNMIATDYKQLQYAVQLNSVDIPLADCHFWTMQGAVAVGELCNEWGMTWGSHSNNHFDISLAMMTHVAAACPGEITAIDTHWIWQDGQRITREPFQIRDGKLTVPKTPGLGIELDDDKLMEAHETYKRLDVTQRNDAMAMQYLIPGWEFDPKRPALVR 441
               SCOP domains d3nfub1 B:1-132 automated matches                                                                                                   d3nfub2 B:133-441 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-3nfuB01 B:215-285                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-3nfuB02 B:215-285                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-3nfuB03 B:285-396                                                                                      --------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-3nfuB04 B:285-396                                                                                      --------------------------------------------- Pfam domains (4)
         Sec.struct. author ....eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh..hhhhh........eee..eeee...hhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..........hhhhhh..............eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfu B   1 LFPKITKMNVVPVAGEDGFLLNLSGGHEPWFIRCVLVLEDESGNRGVGEIPSSEGILNGLEKCRSLVEGARVNEVKQVLSRARGLLAQGGPEERGRQTFDLRVAVHVITAIESALFDLFGQALGMPVADLLGQYGRQRDEVEALGYLFLLGDPDKTDLPYPRVADPVDAWDEVRYREAMTPEAVANLARAAYDRYGFKDFKLKGGVLRGEEEADCIRALHEAFPEARLALDPNGAWKLDEAVRVLEPIKHLLSYAEDPCGQEGGFSGRETMAEFKKRTGLPTATNMIATDYKQLQYAVQLNSVDIPLADCHFWTMQGAVAVGELCNEWGMTWGSHSNNHFDISLAMMTHVAAACPGEITAIDTHWIWQDGQRITREPFQIRDGKLTVPKTPGLGIELDDDKLMEAHETYKRLDVTQRNDAMAMQYLIPGWEFDPKRPALVE 441
                                    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       340       350       360       370       380       390       400       410       420       430       440
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q1QUN0_CHRSD | Q1QUN0)
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:0008872    glucarate dehydratase activity    Catalysis of the reaction: D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O.
    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: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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q1QUN0_CHRSD | Q1QUN0: 3mzn

(-) Related Entries Specified in the PDB File

3mzn CRYSTAL STRUCTURE OF PROBABLE GLUCARATE DEHYDRATASE FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 RELATED ID: NYSGXRC-9499T RELATED DB: TARGETDB