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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-HYDROXYBENZOATE HYDROXYLASE FROM COMAMONAS TESTOSTERONI, IN COMPLEX WITH THE SUBSTRATE
 
Authors :  T. Hiromoto, S. Fujiwara, K. Hosokawa, H. Yamaguchi
Date :  11 Apr 06  (Deposition) - 24 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  3-Hydroxybenzoate Hydroxylase, Flavoprotein, Monooxygenase, Substrate Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hiromoto, S. Fujiwara, K. Hosokawa, H. Yamaguchi
Crystal Structure Of 3-Hydroxybenzoate Hydroxylase From Comamonas Testosteroni Has A Large Tunnel For Substrate And Oxygen Access To The Active Site
J. Mol. Biol. V. 364 878 2006
PubMed-ID: 17045293  |  Reference-DOI: 10.1016/J.JMB.2006.09.031

(-) Compounds

Molecule 1 - 3-HYDROXYBENZOATE HYDROXYLASE
    Chains: A
    EC Number: 1.14.13.23
    Organism Scientific: COMAMONAS TESTOSTERONI
    Organism Taxid: 285
    Strain: KH122-3S
    Synonym: M-HYDROXYBENZOATE HYDROXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
13HB1Ligand/Ion3-HYDROXYBENZOIC ACID
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
13HB2Ligand/Ion3-HYDROXYBENZOIC ACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:3 , HIS A:4 , LEU A:5 , ARG A:9 , HOH A:886 , HOH A:889 , HOH A:1090 , HOH A:1190BINDING SITE FOR RESIDUE SO4 A 642
2AC2SOFTWAREVAL A:487 , GLN A:488 , HIS A:491 , HOH A:853 , HOH A:1001BINDING SITE FOR RESIDUE SO4 A 643
3AC3SOFTWAREGLY A:456 , GLN A:457 , ALA A:458 , LYS A:459 , HOH A:680 , HOH A:755 , HOH A:860 , HOH A:1046BINDING SITE FOR RESIDUE SO4 A 644
4AC4SOFTWAREGLY A:39 , GLY A:41 , PRO A:42 , ALA A:43 , GLU A:63 , GLN A:64 , LYS A:65 , GLN A:73 , GLN A:140 , ARG A:164 , ARG A:165 , VAL A:166 , CYS A:206 , ASP A:207 , GLY A:208 , ASN A:212 , VAL A:232 , ARG A:269 , TYR A:271 , SER A:315 , TYR A:317 , GLY A:348 , ASP A:349 , GLY A:361 , SER A:365 , HOH A:659 , HOH A:668 , HOH A:727 , HOH A:780 , HOH A:815 , HOH A:988 , HOH A:1172BINDING SITE FOR RESIDUE FAD A 640
5AC5SOFTWAREASP A:75 , GLY A:76 , HIS A:135 , ILE A:137 , LYS A:247 , ILE A:260 , TYR A:271 , HOH A:888 , HOH A:1200BINDING SITE FOR RESIDUE 3HB A 641

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:302 -Pro A:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DKH)

(-) 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:614
 aligned with MOBA_COMTE | Q6SSJ6 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:639
                                    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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630         
           MOBA_COMTE     1 MQFHLNGFRPGNPLIAPASPLAPAHTEAVPSQVDVLIVGCGPAGLTLAAQLAAFPDIRTCIVEQKEGPMELGQADGIACRTMEMFEAFEFADSILKEACWINDVTFWKPDPAQPGRIARHGRVQDTEDGLSEFPHVILNQARVHDHYLERMRNSPSRLEPHYARRVLDVKIDHGAADYPVTVTLERCDAAHAGQIETVQARYVVGCDGARSNVRRAIGRQLVGDSANQAWGVMDVLAVTDFPDVRYKVAIQSEQGNVLIIPREGGHLVRFYVEMDKLDADERVASRNITVEQLIATAQRVLHPYKLDVKNVPWWSVYEIGQRICAKYDDVADAVATPDSPLPRVFIAGDACHTHSPKAGQGMNFSMQDSFNLGWKLAAVLRKQCAPELLHTYSSERQVVAQQLIDFDREWAKMFSDPAKEGGQGGVDPKEFQKYFEQHGRFTAGVGTHYAPSLLTGQASHQALASGFTVGMRFHSAPVVRVSDAKPLQLGHCGKADGRWRLYAFAGQNDLAQPESGLLALCRFLESDAASPLRRFTPSGQDIDSIFDLRAIFPQAYTEVALETLPALLLPPKGQLGMIDYEKVFSPDLKNAGQDIFELRGIDRQQGALVVVRPDQYVAQVLPLGDHAALSAYFESFMRA 639
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eeeeeee..hhhhhhhhhhhh......eeee.............eehhhhhhhhhhh.hhhhhhhhheee.eeeeeee.......eeeeeeee..........eee.hhhhhhhhhhhhhhhh.........eeeeeeee........eeeeeee.hhhhh..eeeeeeeeeee.....hhhhhhh....ee......eeeeeeeeee.......eeeeee..eeeeeee......eeeeee..-----------..hhhhhhhhhhhhhh...eeeeeeeeeeee....ee....................eee.hhh.ee.hhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..--------------hhhhhhhhhhhhhhhhh................hhhhhh...........eeee.....eee.hhhh.....eeeeee..........hhhhhhhhhhhhh..hhhhhhh.........eeeeee...hhhhhhhhhhhhhhh.ee....ee....eee........hhhhhh.......eeeee.....eeeee...hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dkh A   1 MQFHLNGFRPGNPLIAPASPLAPAHTEAVPSQVDVLIVGCGPAGLTLAAQLAAFPDIRTCIVEQKEGPMELGQADGIACRTMEMFEAFEFADSILKEACWINDVTFWKPDPGQPGRIARHGRVQDTEDGLSEFPHVILNQARVHDHYLERMRNSPSRLEPHYARRVLDVKVDHGAADYPVTVTLERCDAAHAGQIETVQARYVVGCDGARSNVRRAIGRQLVGDSANQAWGVMDVLAVTDFPDVRYKVAIQSEQGNVLIIPREGGHLVRFYVEMD-----------NITVEQLIATAQRVLHPYKLEVKNVPWWSVYEIGQRICAKYDDVVDAVATPDSPLPRVFIAGDACHTHSPKAGQGMNFSMQDSFNLGWKLAAVLRKQCAPELLHTYSSERQVVAQQLIDFDREWAK--------------DPKEFQKYFEQHGRFTAGVGTHYAPSLLTGQAKHQALASGFTVGMRFHSAPVVRVCDAKPVQLGHCGKADGRWRLYAFAAQNDLAQPESGLLALCRFLEGDAASPLRRFTPAGQDIDSIFDLRAVFPQAYTEVALETLPALLLPPKGQLGMIDYEKVFSPDLKNAGQDIFELRGIDRQQGALVVVRPDQYVAQVLPLGDHAALSAYFESFMRA 639
                                    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    |    -      |290       300       310       320       330       340       350       360       370       380       390       400       410 |       -      |430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630         
                                                                                                                                                                                                                                                                                                            275         287                                                                                                                          412            427
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2DKH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DKH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (MOBA_COMTE | Q6SSJ6)
molecular function
    GO:0018668    3-hydroxybenzoate 4-monooxygenase activity    Catalysis of the reaction: 3-hydroxybenzoate + H(+) + NADPH + O(2) = 3,4-dihydroxybenzoate + H(2)O + NADP(+).
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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UniProtKB/Swiss-Prot
        MOBA_COMTE | Q6SSJ6: 2dki

(-) Related Entries Specified in the PDB File

2dki THE SAME PROTEIN, UNDER PRESSURE OF XENON GAS (12 ATM)