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(-) Description

Title :  A45G P-HYDROXYBENZOATE HYDROXYLASE WITH P-HYDROXYBENZOATE BOUND
 
Authors :  L. J. Cole, D. L. Gatti, B. Entsch, D. P. Ballou
Date :  18 Jan 05  (Deposition) - 26 Jul 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Phbh, Catalysis, Conformations, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Cole, D. L. Gatti, B. Entsch, D. P. Ballou
Removal Of A Methyl Group Causes Global Changes In P-Hydroxybenzoate Hydroxylase.
Biochemistry V. 44 8047 2005
PubMed-ID: 15924424  |  Reference-DOI: 10.1021/BI050108X

(-) Compounds

Molecule 1 - P-HYDROXYBENZOATE HYDROXYLASE
    Chains: A, B
    EC Number: 1.14.13.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIE130 (A DERIVATIVE OF PUC18)
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POBA
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: 4-HYDROXYBENZOATE 3-MONOOXYGENASE, PHBH

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PHB2Ligand/IonP-HYDROXYBENZOIC ACID
3PSL2Ligand/IonPYROSULFATE
4SO412Ligand/IonSULFATE ION
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PHB2Ligand/IonP-HYDROXYBENZOIC ACID
3PSL2Ligand/IonPYROSULFATE
4SO412Ligand/IonSULFATE ION
Biological Unit 2 (4, 36)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PHB4Ligand/IonP-HYDROXYBENZOIC ACID
3PSL4Ligand/IonPYROSULFATE
4SO424Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:1176 , HOH A:3059 , HOH A:3408 , HOH A:3555 , ASP B:2357 , ALA B:2358BINDING SITE FOR RESIDUE SO4 A 701
02AC2SOFTWAREARG B:2085 , ASP B:2087 , LEU B:2088 , LYS B:2089 , ARG B:2090 , HOH B:3322 , HOH B:3415 , HOH B:3417 , HOH B:3473BINDING SITE FOR RESIDUE SO4 B 702
03AC3SOFTWAREPRO B:2248 , SER B:2249 , HOH B:3241 , HOH B:3507 , HOH B:3545BINDING SITE FOR RESIDUE SO4 B 703
04AC4SOFTWARESER A:1235 , ASP A:1236 , LYS A:1263 , HOH A:3106 , HOH A:3158 , HOH A:3359BINDING SITE FOR RESIDUE SO4 A 704
05AC5SOFTWAREVAL A:1071 , HIS A:1072 , GLU A:1073 , GLY A:1074 , ARG A:1085 , GLU A:1198BINDING SITE FOR RESIDUE SO4 A 705
06AC6SOFTWAREASP B:2131 , GLY B:2134 , GLU B:2135 , ARG B:2136 , SER B:2228BINDING SITE FOR RESIDUE SO4 B 706
07AC7SOFTWAREARG B:2042 , ILE B:2043 , ARG B:2044 , ARG B:2220 , GLU B:2262 , SER B:2264 , HOH B:3079 , HOH B:3163 , HOH B:3297BINDING SITE FOR RESIDUE SO4 B 707
08AC8SOFTWARETYR A:1038 , ARG A:1042BINDING SITE FOR RESIDUE SO4 A 708
09AC9SOFTWAREARG A:1042 , ILE A:1043 , ARG A:1044 , ARG A:1220 , GLU A:1262 , SER A:1264 , HOH A:3296 , HOH A:3515BINDING SITE FOR RESIDUE SO4 A 709
10BC1SOFTWAREGLN B:2277 , HIS B:2278 , GLY B:2279 , HOH B:3045 , HOH B:3111 , HOH B:3227 , HOH B:3350BINDING SITE FOR RESIDUE SO4 B 711
11BC2SOFTWARESER B:2235 , ASP B:2236 , LYS B:2263 , HOH B:3239 , HOH B:3395BINDING SITE FOR RESIDUE SO4 B 712
12BC3SOFTWAREGLN B:2133 , PRO B:2170 , ARG B:2173 , HIS B:2278 , HOH B:3434BINDING SITE FOR RESIDUE SO4 B 713
13BC4SOFTWAREILE A:1008 , GLY A:1009 , GLY A:1011 , PRO A:1012 , SER A:1013 , LEU A:1031 , GLU A:1032 , ARG A:1033 , GLN A:1034 , VAL A:1039 , ARG A:1042 , ARG A:1044 , GLY A:1045 , GLY A:1046 , VAL A:1047 , GLN A:1102 , VAL A:1127 , CYS A:1158 , ASP A:1159 , GLY A:1160 , GLY A:1163 , ILE A:1164 , GLY A:1285 , ASP A:1286 , PRO A:1293 , ALA A:1296 , LYS A:1297 , GLY A:1298 , LEU A:1299 , ASN A:1300 , PHB A:1396 , HOH A:3008 , HOH A:3024 , HOH A:3035 , HOH A:3050 , HOH A:3293 , HOH A:3431 , HOH A:3467BINDING SITE FOR RESIDUE FAD A 1395
14BC5SOFTWAREILE B:2008 , GLY B:2009 , GLY B:2011 , PRO B:2012 , SER B:2013 , GLU B:2032 , ARG B:2033 , GLN B:2034 , VAL B:2039 , ARG B:2042 , ARG B:2044 , GLY B:2045 , GLY B:2046 , VAL B:2047 , GLN B:2102 , CYS B:2158 , ASP B:2159 , GLY B:2160 , GLY B:2163 , ASP B:2286 , PRO B:2293 , ALA B:2296 , LYS B:2297 , GLY B:2298 , LEU B:2299 , ASN B:2300 , PHB B:2396 , HOH B:3005 , HOH B:3007 , HOH B:3017 , HOH B:3019 , HOH B:3020 , HOH B:3023 , HOH B:3030 , HOH B:3033 , HOH B:3125 , HOH B:3440BINDING SITE FOR RESIDUE FAD B 2395
15BC6SOFTWAREARG A:1044 , GLY A:1045 , GLY A:1046 , TRP A:1185 , LEU A:1199 , TYR A:1201 , LEU A:1210 , SER A:1212 , ARG A:1214 , ARG A:1220 , TYR A:1222 , PRO A:1293 , THR A:1294 , ALA A:1296 , FAD A:1395BINDING SITE FOR RESIDUE PHB A 1396
16BC7SOFTWAREARG B:2044 , GLY B:2045 , GLY B:2046 , TYR B:2201 , LEU B:2210 , SER B:2212 , ARG B:2214 , ARG B:2220 , TYR B:2222 , PRO B:2293 , THR B:2294 , ALA B:2296 , FAD B:2395BINDING SITE FOR RESIDUE PHB B 2396
17BC8SOFTWAREARG B:2128 , HIS B:2162 , PRO B:2267 , ARG B:2269 , HOH B:3190 , HOH B:3424 , HOH B:3506BINDING SITE FOR RESIDUE PSL B 714
18BC9SOFTWAREARG B:2033 , GLN B:2034 , ALA B:2125 , GLU B:2126 , ARG B:2128 , HOH B:3019 , HOH B:3436 , HOH B:3440 , HOH B:3471BINDING SITE FOR RESIDUE PSL B 715

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YKJ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:1274 -Pro A:1275
2Glu B:2274 -Pro B:2275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YKJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YKJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1YKJ)

(-) 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:394
 aligned with PHHY_PSEAE | P20586 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    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    
          PHHY_PSEAE      1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE  394
               SCOP domains d1ykja1 A:1001-1173,A:1276-1394 p-Hydroxybenzoate hydroxylase, PHBH                                                                                                          d1ykja2 A:1174-1275 p-Hydroxybenzoate hydroxylase (PHBH)                                              d1ykja1 A:1001-1173,A:1276-1394 p-Hydroxybenzoate hydroxylase, PHBH                                                     SCOP domains
               CATH domains 1ykjA01 A:1001-1073,A:1096-1180,A:1269-1351                              1ykjA02               1ykjA01 A:1001-1073,A:1096-1180,A:1269-1351  [code=3.50.50.60, no name defined]      1ykjA02 A:1074-1095,A:1181-1268,A:1352-1388 D-Amino Acid Oxidase, subunit A, domain 2   1ykjA01 A:1001-1073,A:1096-1180,A:1269-1351  [code=3.50.50.60, no name defined]    1ykjA02                              ------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee...hhhhhh......eeehhhhhhhhhh..hhhhhhhheee.eeeee....eeeeehhhhhh...eee.hhhhhhhhhhhhhhhhh.eee...eeeeee.......eeeeee..eeeeee..eeee.......hhhhhhhhhheeeeeeeeeeeeeeee.........eee......eeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeeeeee..ee..eee.hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ykj A 1001 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRGGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE 1394
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390    


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with PHHY_PSEAE | P20586 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    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    
          PHHY_PSEAE      1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE  394
               SCOP domains d1ykjb1 B:2001-2173,B:2276-2394 p-Hydroxybenzoate hydroxylase, PHBH                                                                                                          d1ykjb2 B:2174-2275 p-Hydroxybenzoate hydroxylase (PHBH)                                              d1ykjb1 B:2001-2173,B:2276-2394 p-Hydroxybenzoate hydroxylase, PHBH                                                     SCOP domains
               CATH domains 1ykjB01 B:2001-2073,B:2096-2180,B:2269-2351                              1ykjB02               1ykjB01 B:2001-2073,B:2096-2180,B:2269-2351  [code=3.50.50.60, no name defined]      1ykjB02 B:2074-2095,B:2181-2268,B:2352-2388 D-Amino Acid Oxidase, subunit A, domain 2   1ykjB01 B:2001-2073,B:2096-2180,B:2269-2351  [code=3.50.50.60, no name defined]    1ykjB02                              ------ CATH domains
           Pfam domains (1) -FAD_binding_3-1ykjB01 B:2002-2343                                                                                                                                                                                                                                                                                                                     --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -FAD_binding_3-1ykjB02 B:2002-2343                                                                                                                                                                                                                                                                                                                     --------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee...hhhhhhh.....eehhhhhhhhhhh........--.eee.eeeee..eeeeehhhhhh....eee.hhhhhhhhhhhhhhh...eee...eeeeee.......eeeeee..eeeeee..eeee.......hhhhhhhhhheeeeeeeeeeeeeeee........eeeee.....eeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeeee..ee..eee.hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ykj B 2001 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRGGVLEQGMVDLLREAGVDRRMAR--LVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE 2394
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280      2290      2300      2310      2320      2330      2340      2350      2360      2370      2380      2390    
                                                                                           2067  |                                                                                                                                                                                                                                                                                                                                    
                                                                                              2070
   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: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHHY_PSEAE | P20586)
molecular function
    GO:0018659    4-hydroxybenzoate 3-monooxygenase activity    Catalysis of the reaction: 4-hydroxybenzoate + NADPH + H+ + O2 = protocatechuate + NADP+ + H2O.
    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:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0043639    benzoate catabolic process    The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.
    GO:0043640    benzoate catabolic process via hydroxylation    The chemical reactions and pathways resulting in the breakdown of benzoate, by its hydroxylation to cis-1,2-dihydroxybenzoate followed by dehydrogenation to catechol.
    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.
    GO:0044550    secondary metabolite biosynthetic process    The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon.

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  1ykj
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    Protein Cavities: castP
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PHHY_PSEAE | P20586
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PHHY_PSEAE | P20586: 1d7l 1dob 1doc 1dod 1doe 1ius 1iut 1iuu 1iuv 1iuw 1iux 1k0i 1k0j 1k0l 1pxa 1pxb 1pxc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YKJ)