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(-) Description

Title :  CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-ARABINOHYDROXAMATE
 
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 :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Uronate Isomerase, D-Arabinohydroxamate, 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
    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

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CO32Ligand/IonCARBONATE ION
3HDL2Ligand/IonD-ARABINOHYDROXAMIC ACID
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CO36Ligand/IonCARBONATE ION
3HDL6Ligand/IonD-ARABINOHYDROXAMIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CO36Ligand/IonCARBONATE ION
3HDL6Ligand/IonD-ARABINOHYDROXAMIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:26 , HIS A:28 , HIS A:49 , TYR A:50 , ARG A:170 , TRP A:325 , TRP A:326 , ASP A:355 , ARG A:357 , ZN A:430 , HOH A:596 , HOH A:600 , HOH A:627BINDING SITE FOR RESIDUE HDL A 428
02AC2SOFTWAREHIS A:49 , TYR A:50 , ARG A:314 , LYS A:315 , TRP A:326 , PHE A:327 , HOH A:571BINDING SITE FOR RESIDUE CO3 A 429
03AC3SOFTWAREHIS A:26 , HIS A:28 , ASP A:355 , HDL A:428BINDING SITE FOR RESIDUE ZN A 430
04AC4SOFTWAREHOH A:593 , HOH A:594BINDING SITE FOR RESIDUE ZN A 431
05AC5SOFTWARELYS A:278 , GLU A:304BINDING SITE FOR RESIDUE CL A 432
06AC6SOFTWAREHIS B:26 , HIS B:28 , HIS B:49 , TYR B:50 , ARG B:170 , TRP B:325 , TRP B:326 , ASP B:355 , ARG B:357 , ZN B:430 , HOH B:525 , HOH B:532 , HOH B:549BINDING SITE FOR RESIDUE HDL B 428
07AC7SOFTWAREHIS B:49 , TYR B:50 , ARG B:314 , LYS B:315 , TRP B:326 , PHE B:327 , HOH B:475BINDING SITE FOR RESIDUE CO3 B 429
08AC8SOFTWAREHIS B:26 , HIS B:28 , ASP B:355 , HDL B:428BINDING SITE FOR RESIDUE ZN B 430
09AC9SOFTWAREHOH B:522 , HOH B:523BINDING SITE FOR RESIDUE ZN B 431
10BC1SOFTWARELYS B:278 , GLU B:304BINDING SITE FOR RESIDUE CL B 432

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HK8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:230 -Pro A:231
2Phe B:230 -Pro B:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HK8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HK8)

(-) Exons   (0, 0)

(no "Exon" information available for 3HK8)

(-) 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:409
 aligned with Q9KFI6_BACHD | Q9KFI6 from UniProtKB/TrEMBL  Length:427

    Alignment length:409
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404         
         Q9KFI6_BACHD     5 SREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
               SCOP domains d3hk8a_ A: Uncharacterized protein BH0493                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------3hk8A02 A:39-120 uronate isomerase, domain 2, chain A                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eee......hhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhheeeee......hhhhhhhhhhh......ee..eehhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.ee...hhhhhhhhhee....hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hk8 A   5 SREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404         


Chain B from PDB  Type:PROTEIN  Length:409
 aligned with Q9KFI6_BACHD | Q9KFI6 from UniProtKB/TrEMBL  Length:427

    Alignment length:409
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404         
         Q9KFI6_BACHD     5 SREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
               SCOP domains d3hk8b_ B: Uncharacterized protein BH0493                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------3hk8B02 B:39-120 uronate isomerase, domain 2, chain A                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eee......hhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhheeeee......hhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.ee...hhhhhhhhhee....hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hk8 B   5 SREVLAEKVKNAVNNQPVTDMHTHLFSPNFGEILLWDIDELLTYHYLVAEVMRWTDVSIEAFWAMSKREQADLIWEELFIKRSPVSEACRGVLTCLQGLGLDPATRDLQVYREYFAKKTSEEQVDTVLQLANVSDVVMTNDPFDDNERISWLEGKQPDSRFHAALRLDPLLNEYEQTKHRLRDWGYKVNDEWNEGSIQEVKRFLTDWIERMDPVYMAVSLPPTFSFPEESNRGRIIRDCLLPVAEKHNIPFAMMIGVKKRVHPALGDAGDFVGKASMDGVEHLLREYPNNKFLVTMLSRENQHELVVLARKFSNLMIFGCWWFMNNPEIINEMTRMRMEMLGTSFIPQHSDARVLEQLIYKWHHSKSIIAEVLIDKYDDILQAGWEVTEEEIKRDVADLFSRNFWRFVG 413
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HK8)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3hk8
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  Q9KFI6_BACHD | Q9KFI6
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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 3hk9 3hka

(-) 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
3hk9 CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-GLUCURONATE
3hka CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-FRUCTURONATE