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(-) Description

Title :  CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-FRUCTURONATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, T. T. Nguyen, F. M. Raushel, S. C. Almo
Date :  22 May 09  (Deposition) - 25 Aug 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Uronate Isomerase, D-Fructuronate, Mechanism Of The Reaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. T. Nguyen, A. A. Fedorov, L. Williams, E. V. Fedorov, Y. Li, C. Xu, S. C. Almo, F. M. Raushel
The Mechanism Of The Reaction Catalyzed By Uronate Isomerase Illustrates How An Isomerase May Have Evolved From A Hydrolase Within The Amidohydrolase Superfamily.
Biochemistry V. 48 8879 2009
PubMed-ID: 19678710  |  Reference-DOI: 10.1021/BI901046X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URONATE ISOMERASE
    Atcc: BAA-125
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BH0493
    Organism Scientific: BACILLUS HALODURANS C-125
    Organism Taxid: 272558
    Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153
    Synonym: BH0493 PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CO33Ligand/IonCARBONATE ION
3FIX3Ligand/IonD-FRUCTURONIC ACID
4ZN4Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:26 , HIS A:28 , HIS A:49 , TYR A:50 , ARG A:170 , MET A:258 , TRP A:325 , TRP A:326 , ASP A:355 , ARG A:357 , ZN A:430 , HOH A:549 , HOH A:566 , HOH A:581BINDING SITE FOR RESIDUE FIX A 428
02AC2SOFTWAREARG A:314 , LYS A:315 , HIS C:49 , TYR C:50 , TRP C:326 , PHE C:327 , HOH C:445BINDING SITE FOR RESIDUE CO3 A 429
03AC3SOFTWAREHIS A:26 , HIS A:28 , ASP A:355 , FIX A:428BINDING SITE FOR RESIDUE ZN A 430
04AC4SOFTWARELYS A:278 , GLU A:304 , LYS B:278 , GLU B:304 , LYS C:278 , GLU C:304BINDING SITE FOR RESIDUE CL A 431
05AC5SOFTWAREHIS B:26 , HIS B:28 , HIS B:49 , TYR B:50 , ARG B:170 , MET B:258 , TRP B:325 , TRP B:326 , ASP B:355 , ARG B:357 , ZN B:431 , HOH B:499 , HOH B:508 , HOH B:595 , HOH B:596BINDING SITE FOR RESIDUE FIX B 428
06AC6SOFTWAREHIS A:49 , TYR A:50 , TRP A:326 , PHE A:327 , HOH A:447 , ARG B:314 , LYS B:315BINDING SITE FOR RESIDUE CO3 B 429
07AC7SOFTWAREHIS B:49 , TYR B:50 , TRP B:326 , PHE B:327 , HOH B:441 , ARG C:314 , LYS C:315BINDING SITE FOR RESIDUE CO3 B 430
08AC8SOFTWAREHIS B:26 , HIS B:28 , ASP B:355 , FIX B:428BINDING SITE FOR RESIDUE ZN B 431
09AC9SOFTWAREHIS C:26 , HIS C:28 , HIS C:49 , TYR C:50 , ARG C:170 , MET C:258 , TRP C:325 , TRP C:326 , ASP C:355 , ARG C:357 , ZN C:429 , HOH C:544 , HOH C:560 , HOH C:563BINDING SITE FOR RESIDUE FIX C 428
10BC1SOFTWAREHIS C:26 , HIS C:28 , ASP C:355 , FIX C:428BINDING SITE FOR RESIDUE ZN C 429
11BC2SOFTWAREHOH A:468 , HOH A:579 , HOH B:582 , HOH B:583 , HOH C:581 , HOH C:600BINDING SITE FOR RESIDUE ZN C 430

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:230 -Pro A:231
2Phe B:230 -Pro B:231
3Phe C:230 -Pro C:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HKA)

(-) 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:411
 aligned with Q9KFI6_BACHD | Q9KFI6 from UniProtKB/TrEMBL  Length:427

    Alignment length:411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 
         Q9KFI6_BACHD     3 INSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
               SCOP domains d3hkaa_ A: Uncharacterized protein BH0493                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------3hkaA02 A:39-120 uronate isomerase, domain 2, chain A                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.eee......hhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.ee...hhhhhhhh.ee....hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hka A   3 INSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 


Chain B from PDB  Type:PROTEIN  Length:411
 aligned with Q9KFI6_BACHD | Q9KFI6 from UniProtKB/TrEMBL  Length:427

    Alignment length:411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 
         Q9KFI6_BACHD     3 INSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
               SCOP domains d3hkab_ B: Uncharacterized protein BH0493                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------3hkaB02 B:39-120 uronate isomerase, domain 2, chain A                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.eee......hhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhh.eeeee......hhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.ee...hhhhhhhh.ee....hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hka B   3 INSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 


Chain C from PDB  Type:PROTEIN  Length:411
 aligned with Q9KFI6_BACHD | Q9KFI6 from UniProtKB/TrEMBL  Length:427

    Alignment length:411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 
         Q9KFI6_BACHD     3 INSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
               SCOP domains d3hkac_ C: Uncharacterized protein BH0493                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------3hkaC02 C:39-120 uronate isomerase, domain 2, chain A                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.eee......hhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.ee...hhhhhhhh.ee....hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hka C   3 INSREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

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

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HKA)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q9KFI6_BACHD | Q9KFI6)
molecular function
    GO:0008880    glucuronate isomerase activity    Catalysis of the reaction: D-glucuronate = D-fructuronate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3hka
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 Related Entries

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

UniProtKB/TrEMBL
        Q9KFI6_BACHD | Q9KFI6: 2pnk 2q08 2q6e 2qee 3hk5 3hk7 3hk8 3hk9

(-) Related Entries Specified in the PDB File

2q08 CRYSTAL STRUCTURE OF URONATE ISOMERASE IN APO FORM
2q6e CRYSTAL STRUCTURE OF URONATE ISOMERASE IN APO FORM
3hk5 CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-ARABINARATE, CRYSTAL FORM 1
3hk7 CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-ARABINARATE, CRYSTAL FORM 2
3hk8 CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-ARABINOHYDROXAMATE
3hk9 CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-GLUCURONATE