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(-) Description

Title :  L-FUCOSE ISOMERASE IN COMPLEX WITH FUCITOL
 
Authors :  M. A. Higgins, M. D. L. Suits, C. Marsters, A. B. Boraston
Date :  16 Aug 13  (Deposition) - 11 Dec 13  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Fucose Processing, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Higgins, M. D. Suits, C. Marsters, A. B. Boraston
Structural And Functional Analysis Of Fucose-Processing Enzymes From Streptococcus Pneumoniae.
J. Mol. Biol. V. 426 1469 2014
PubMed-ID: 24333485  |  Reference-DOI: 10.1016/J.JMB.2013.12.006

(-) Compounds

Molecule 1 - L-FUCOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: 6-DEOXY-L-GALACTOSE ISOMERASE, FUCIASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2FOC2Ligand/IonFUCITOL
3MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 54)
No.NameCountTypeFull Name
1EDO48Ligand/Ion1,2-ETHANEDIOL
2FOC6Ligand/IonFUCITOL
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:335 , ASP A:359 , ASN A:390 , SER A:391 , HIS A:525 , FOC A:601BINDING SITE FOR RESIDUE MN A 600
02AC2SOFTWAREARG A:16 , TRP A:88 , PRO A:114 , MET A:183 , GLN A:300 , GLU A:335 , ASP A:359 , SER A:391 , TYR A:437 , ASN A:524 , HIS A:525 , MN A:600BINDING SITE FOR RESIDUE FOC A 601
03AC3SOFTWAREGLU B:335 , ASP B:359 , HIS B:525 , FOC B:601 , HOH B:2216BINDING SITE FOR RESIDUE MN B 600
04AC4SOFTWAREARG B:16 , TRP B:88 , GLN B:300 , GLU B:335 , ASP B:359 , SER B:391 , TYR B:437 , ASN B:524 , HIS B:525 , MN B:600 , HOH B:2224BINDING SITE FOR RESIDUE FOC B 601
05AC5SOFTWAREILE B:538 , ALA B:541 , SER B:542 , ILE B:546 , PRO B:547 , VAL B:548 , ARG B:560 , ASP B:576 , CYS B:580BINDING SITE FOR RESIDUE EDO B1589
06AC6SOFTWAREGLU A:197 , TYR A:198 , GLY A:467 , HOH A:2134 , HOH A:2269BINDING SITE FOR RESIDUE EDO A1589
07AC7SOFTWAREPRO A:99 , ARG B:171 , ASP B:172 , HIS B:587BINDING SITE FOR RESIDUE EDO B1590
08AC8SOFTWARELEU A:119 , ASN A:519 , LYS A:562 , HOH A:2290BINDING SITE FOR RESIDUE EDO A1590
09AC9SOFTWARETHR A:209 , THR A:212 , TRP A:303 , PHE A:307 , THR B:209 , THR B:212 , TRP B:303 , PHE B:307BINDING SITE FOR RESIDUE EDO B1591
10BC1SOFTWAREASP B:193 , PHE B:194 , GLU B:197 , TYR B:198 , GLY B:467 , HOH B:2132 , HOH B:2266BINDING SITE FOR RESIDUE EDO B1592
11BC2SOFTWARELEU B:119 , GLY B:135 , ASN B:519 , LYS B:562 , HOH B:2294BINDING SITE FOR RESIDUE EDO B1593
12BC3SOFTWAREHIS A:551 , GLU A:555 , GLU A:570 , HOH A:2302 , HOH A:2323BINDING SITE FOR RESIDUE EDO A1591
13BC4SOFTWARETYR A:476 , ARG A:504BINDING SITE FOR RESIDUE EDO A1592
14BC5SOFTWAREARG B:159 , GLU B:556 , ASP B:557 , PHE B:559BINDING SITE FOR RESIDUE EDO B1594
15BC6SOFTWAREALA B:116 , VAL B:117 , ALA B:120 , VAL B:360 , MET B:518 , TRP B:521 , ALA B:523 , ASN B:524 , HOH B:2294BINDING SITE FOR RESIDUE EDO B1595
16BC7SOFTWAREARG B:504 , PRO B:554BINDING SITE FOR RESIDUE EDO B1596
17BC8SOFTWARETHR B:42 , LEU B:43 , LYS B:44 , ASN B:352 , HOH B:2219BINDING SITE FOR RESIDUE EDO B1597
18BC9SOFTWAREGLU B:556 , ASP B:557BINDING SITE FOR RESIDUE EDO B1598
19CC1SOFTWAREARG A:217 , ARG B:435 , ARG B:439BINDING SITE FOR RESIDUE EDO B1599
20CC2SOFTWAREARG A:435 , ARG A:439 , ARG B:217BINDING SITE FOR RESIDUE EDO A1593

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C21)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:300 -Arg A:301
2Gln B:300 -Arg B:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C21)

(-) Exons   (0, 0)

(no "Exon" information available for 4C21)

(-) 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:587
 aligned with FUCI_STRPN | Q97N97 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:587
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       
           FUCI_STRPN     2 IQHPRIGIRPTIDGRRQGVRESLEVQTMNMAKSVADLISSTLKYPDGEPVECVISPSTIGRVPEAAASHELFKKSNVCATITVTPCWCYGSETMDMSPDIPHAIWGFNGTERPGAVYLAAVLASHAQKGIPAFGIYGRDVQEASDTDIPEDVKEKLLRYARAALATGLMRDTAYLSMGSVSMGIGGSIVNPDFFQEYLGMRNESVDMTEFTRRMDRGIYDPEEFERALKWVKENVKEGFDHNREDLVLSREEKDRQWEFVIKMFMIGRDLMVGNPRLAELGFEEEAVGHHALVAGFQGQRQWTDHFPNGDFMETFLNTQFDWNGIRKPFVFATENDSLNGVSMLFNYLLTNTPQIFADVRTYWSPEAVKRVTGHTLEGRAAAGFLHLINSGSCTLDGTGQATRDGKPIMKPFWELEESEVQAMLENTDFPPANREYFRGGGFSTRFLTKGDMPVTMVRLNLLKGVGPVLQIAEGYTLELPEDVHHTLDNRTDPGWPTTWFAPRLTGKGAFKSVYDVMNNWGANHGAITYGHIGADLITLASMLRIPVNMHNVPEEDIFRPKNWSLFGTEDLESADYRACQLLGPLHK 588
               SCOP domains d4c21a1 A:2-353 automated matches                                                                                                                                                                                                                                                                                                                               d4c21a2 A:354-588 automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh.........eee......hhhhhhhhhhhhhh..eeeeeeee....hhhhhh.......eeeee......hhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhh.hhhhhhhhhh.eeeee.hhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..eeeeee............hhhhhhhhhh.ee..ee....eeee..hhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhh...hhhhh..eeee......hhhhhh.eee..eee..hhhhhhhhhhhhhhhh..........................eeeeeeeeee...eeeeeeeeeee...hhhhhhhhhhh.......eeeee.........hhhhhhhh....eeeeee..hhhhhhhhhhhh.........hhhhh..hhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c21 A   2 IQHPRIGIRPTIDGRRQGVRESLEVQTMNMAKSVADLISSTLKYPDGEPVECVISPSTIGRVPEAAASHELFKKSNVCATITVTPCWCYGSETMDMSPDIPHAIWGFNGTERPGAVYLAAVLASHAQKGIPAFGIYGRDVQEASDTDIPEDVKEKLLRYARAALATGLMRDTAYLSMGSVSMGIGGSIVNPDFFQEYLGMRNESVDMTEFTRRMDRGIYDPEEFERALKWVKENVKEGFDHNREDLVLSREEKDRQWEFVIKMFMIGRDLMVGNPRLAELGFEEEAVGHHALVAGFQGQRQWTDHFPNGDFMETFLNTQFDWNGIRKPFVFATENDSLNGVSMLFNYLLTNTPQIFADVRTYWSPEAVKRVTGHTLEGRAAAGFLHLINSGSCTLDGTGQATRDGKPIMKPFWELEESEVQAMLENTDFPPANREYFRGGGFSTRFLTKGDMPVTMVRLNLLKGVGPVLQIAEGYTLELPEDVHHTLDNRTDPGWPTTWFAPRLTGKGAFKSVYDVMNNWGANHGAITYGHIGADLITLASMLRIPVNMHNVPEEDIFRPKNWSLFGTEDLESADYRACQLLGPLHK 588
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       


Chain B from PDB  Type:PROTEIN  Length:605
 aligned with FUCI_STRPN | Q97N97 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:605
                                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                     -       | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583     
           FUCI_STRPN     - -----------------MIQHPRIGIRPTIDGRRQGVRESLEVQTMNMAKSVADLISSTLKYPDGEPVECVISPSTIGRVPEAAASHELFKKSNVCATITVTPCWCYGSETMDMSPDIPHAIWGFNGTERPGAVYLAAVLASHAQKGIPAFGIYGRDVQEASDTDIPEDVKEKLLRYARAALATGLMRDTAYLSMGSVSMGIGGSIVNPDFFQEYLGMRNESVDMTEFTRRMDRGIYDPEEFERALKWVKENVKEGFDHNREDLVLSREEKDRQWEFVIKMFMIGRDLMVGNPRLAELGFEEEAVGHHALVAGFQGQRQWTDHFPNGDFMETFLNTQFDWNGIRKPFVFATENDSLNGVSMLFNYLLTNTPQIFADVRTYWSPEAVKRVTGHTLEGRAAAGFLHLINSGSCTLDGTGQATRDGKPIMKPFWELEESEVQAMLENTDFPPANREYFRGGGFSTRFLTKGDMPVTMVRLNLLKGVGPVLQIAEGYTLELPEDVHHTLDNRTDPGWPTTWFAPRLTGKGAFKSVYDVMNNWGANHGAITYGHIGADLITLASMLRIPVNMHNVPEEDIFRPKNWSLFGTEDLESADYRACQLLGPLHK 588
               SCOP domains d4c21b1 B:-16-353 automated matches                                                                                                                                                                                                                                                                                                                                               d4c21b2 B:354-588 automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....ee............eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhhhhhh..eeeeeeee....hhhhhh.......eeeee......hhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhh.hhhhhhhhhh.eeeee.hhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..eeeeee............hhhhhhhhhh.ee..ee....eeee..hhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhh...hhhhh..eeee......hhhhhh.eee..eee..hhhhhhhhhhhhhhhh..........................eeeeeeeeee...eeeeeeeeeee...hhhhhhhhhhh.......eeeee.........hhhhhhhh....eeeeee..hhhhhhhhhhhh.........hhhhh..hhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c21 B -16 HHHHHSSGLVPRGAHMAMIQHPRIGIRPTIDGRRQGVRESLEVQTMNMAKSVADLISSTLKYPDGEPVECVISPSTIGRVPEAAASHELFKKSNVCATITVTPCWCYGSETMDMSPDIPHAIWGFNGTERPGAVYLAAVLASHAQKGIPAFGIYGRDVQEASDTDIPEDVKEKLLRYARAALATGLMRDTAYLSMGSVSMGIGGSIVNPDFFQEYLGMRNESVDMTEFTRRMDRGIYDPEEFERALKWVKENVKEGFDHNREDLVLSREEKDRQWEFVIKMFMIGRDLMVGNPRLAELGFEEEAVGHHALVAGFQGQRQWTDHFPNGDFMETFLNTQFDWNGIRKPFVFATENDSLNGVSMLFNYLLTNTPQIFADVRTYWSPEAVKRVTGHTLEGRAAAGFLHLINSGSCTLDGTGQATRDGKPIMKPFWELEESEVQAMLENTDFPPANREYFRGGGFSTRFLTKGDMPVTMVRLNLLKGVGPVLQIAEGYTLELPEDVHHTLDNRTDPGWPTTWFAPRLTGKGAFKSVYDVMNNWGANHGAITYGHIGADLITLASMLRIPVNMHNVPEEDIFRPKNWSLFGTEDLESADYRACQLLGPLHK 588
                                    -7         3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C21)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C21)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FUCI_STRPN | Q97N97)
molecular function
    GO:0008736    L-fucose isomerase activity    Catalysis of the reaction: L-fucose = L-fuculose.
    GO:0016861    intramolecular oxidoreductase activity, interconverting aldoses and ketoses    Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears.
    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.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0042355    L-fucose catabolic process    The chemical reactions and pathways resulting in the breakdown of L-fucose (6-deoxy-Lgalactose).
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019317    fucose catabolic process    The chemical reactions and pathways resulting in the breakdown of fucose (6-deoxygalactose).
    GO:0006004    fucose metabolic process    The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.
    GO:0005996    monosaccharide metabolic process    The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  4c21
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  FUCI_STRPN | Q97N97
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 Related Entries

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

UniProtKB/Swiss-Prot
        FUCI_STRPN | Q97N97: 4c20 4c22

(-) Related Entries Specified in the PDB File

4c20 L-FUCOSE ISOMERASE
4c22 L-FUCOSE ISOMERASE IN COMPLEX WITH FUCULOSE
4c23 L-FUCULOSE KINASE
4c24 L-FUCULOSE 1-PHOSPHATE ALDOLASE
4c25 L-FUCULOSE 1-PHOSPHATE ALDOLASE