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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AQUIFEX REACTOR COMPLEX FORMED BY DIHYDROOROTASE (H180A, H232A) WITH DIHYDROOROTATE AND ASPARTATE TRANSCARBAMOYLASE WITH N-(PHOSPHONACETYL)-L-ASPARTATE (PALA)
 
Authors :  B. F. P. Edwards, P. D. Martin, E. Grimley, A. Vaishnav, R. Fernando, J. S. Brunzelle, M. Cordes, H. G. Evans, D. R. Evans
Date :  18 Apr 13  (Deposition) - 18 Dec 13  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (6x)
Keywords :  Hydrolase-Transferase Complex, Pyrimidine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. F. Edwards, R. Fernando, P. D. Martin, E. Grimley, M. Cordes, A. Vaishnav, J. S. Brunzelle, H. G. Evans, D. R. Evans
The Mononuclear Metal Center Of Type-I Dihydroorotase From Aquifex Aeolicus.
Bmc Biochem. V. 14 36 2013
PubMed-ID: 24314009  |  Reference-DOI: 10.1186/1471-2091-14-36
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    Chains: A
    EC Number: 3.5.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAAPYRC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PRSETC
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Other Details: GIFT FROM DRS KARL O. STETTER AND ROBERT HUBER, REGENSBURG UNIVERSITY, D-93053 REGENSBURG, GERMANY
    Synonym: DHOASE
 
Molecule 2 - ASPARTATE CARBAMOYLTRANSFERASE
    Chains: B
    EC Number: 2.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAAPYRB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PRSETC
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Other Details: GIFT FROM DRS KARL O. STETTER AND ROBERT HUBER, REGENSBURG UNIVERSITY, D-93053 REGENSBURG, GERMANY
    Synonym: ASPARTATE TRANSCARBAMYLASE, ATCASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (6x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric Unit (6, 19)
No.NameCountTypeFull Name
1BA3Ligand/IonBARIUM ION
2DOR1Ligand/Ion(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
3EDO12Ligand/Ion1,2-ETHANEDIOL
4PAL1Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
5PO41Ligand/IonPHOSPHATE ION
6ZN1Ligand/IonZINC ION
Biological Unit 1 (4, 90)
No.NameCountTypeFull Name
1BA-1Ligand/IonBARIUM ION
2DOR6Ligand/Ion(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
3EDO72Ligand/Ion1,2-ETHANEDIOL
4PAL6Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
5PO46Ligand/IonPHOSPHATE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:61 , HIS A:63 , ASP A:153 , ASP A:305 , HOH A:2018BINDING SITE FOR RESIDUE ZN A 423
02AC2SOFTWAREHIS A:63 , ARG A:65 , ASN A:95 , ASP A:153 , GLY A:154 , VAL A:277 , ASN A:278 , HIS A:309 , PRO A:322 , GLY A:323 , HOH A:2018 , HOH A:2081 , HOH A:2174 , HOH A:2216BINDING SITE FOR RESIDUE DOR A 425
03AC3SOFTWARESER B:45 , THR B:46 , ARG B:47 , THR B:48 , SER B:72 , LYS B:75 , ARG B:97 , HIS B:126 , ARG B:159 , VAL B:160 , ARG B:213 , GLN B:215 , GLY B:251 , HOH B:2059 , HOH B:2139 , HOH B:2140 , HOH B:2166BINDING SITE FOR RESIDUE PAL B 292
04AC4SOFTWAREPHE B:196 , ASP B:197 , ASP B:198 , LYS B:201 , EDO B:305 , EDO B:309BINDING SITE FOR RESIDUE PO4 B 293
05AC5SOFTWAREGLU B:70 , BA B:296 , HOH B:2075 , HOH B:2080BINDING SITE FOR RESIDUE BA B 295
06AC6SOFTWAREGLU B:70 , BA B:295 , EDO B:303BINDING SITE FOR RESIDUE BA B 296
07AC7SOFTWAREASP B:9 , GLU B:14 , EDO B:306BINDING SITE FOR RESIDUE BA B 297
08AC8SOFTWAREASP A:101 , ASN A:102 , THR A:103 , ASP A:138 , HOH B:2182BINDING SITE FOR RESIDUE EDO B 301
09AC9SOFTWAREARG B:47 , GLU B:77 , ASP B:81 , PRO B:252 , VAL B:253 , TYR B:265 , ILE B:271 , HOH B:2097BINDING SITE FOR RESIDUE EDO B 302
10BC1SOFTWAREARG B:49 , LEU B:65 , VAL B:66 , SER B:67 , GLU B:70 , BA B:296BINDING SITE FOR RESIDUE EDO B 303
11BC2SOFTWAREGLU B:43 , PRO B:99 , GLU B:217 , ARG B:218 , HOH B:2177BINDING SITE FOR RESIDUE EDO B 304
12BC3SOFTWAREVAL B:195 , PO4 B:293 , HOH B:2128BINDING SITE FOR RESIDUE EDO B 305
13BC4SOFTWARESER B:3 , ASP B:9 , PHE B:288 , BA B:297BINDING SITE FOR RESIDUE EDO B 306
14BC5SOFTWAREASP A:101 , ASN A:102BINDING SITE FOR RESIDUE EDO B 307
15BC6SOFTWAREARG B:12 , GLU B:13 , GLU B:16BINDING SITE FOR RESIDUE EDO B 308
16BC7SOFTWAREVAL B:195 , ASP B:197 , PO4 B:293BINDING SITE FOR RESIDUE EDO B 309
17BC8SOFTWAREGLN A:222 , GLU A:240 , HOH A:2138BINDING SITE FOR RESIDUE EDO B 310
18BC9SOFTWARETYR A:140 , ASP B:198 , VAL B:199 , ASP B:200 , GLN B:233 , ARG B:240 , HOH B:2154BINDING SITE FOR RESIDUE EDO B 311
19CC1SOFTWARELEU A:200 , HOH A:2119 , SER B:6 , LEU B:8 , TYR B:105 , HIS B:124 , HOH B:2011BINDING SITE FOR RESIDUE EDO B 312

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:66 -Pro A:67
2Asn A:97 -Pro A:98
3Asp A:153 -Gly A:154
4Asn A:278 -Pro A:279
5Phe B:103 -Pro B:104
6Gly B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_AQUAE41-48  1B:41-48
2DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYRC_AQUAE59-67  1A:59-67
3DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYRC_AQUAE303-314  1A:303-314
Biological Unit 1 (3, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_AQUAE41-48  6B:41-48
2DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYRC_AQUAE59-67  6A:59-67
3DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYRC_AQUAE303-314  6A:303-314

(-) Exons   (0, 0)

(no "Exon" information available for 4BJH)

(-) 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:422
 aligned with PYRC_AQUAE | O66990 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:422
                                    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  
           PYRC_AQUAE     1 MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeehhhheeee.eeeee..eeeeee........eeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee.....hhhh.....hhhhhhhhh............hhhhhhhhhhhhhhh...eee...........ee.hhhhhhhh..eehhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeehhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhh....ee.......hhhhh.hhhhh........hhhhhhhhhhhh...hhhhhhhh.hhhhhhhhh.............eeeeeeeeeee..................eeeeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------DIHYDROOR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bjh A   1 MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDACEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQAVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
                                    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  


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with PYRB_AQUAE | O66726 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:291
                                    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 
           PYRB_AQUAE     1 MRSLISSLDLTREEVEEILKYAKEFKEGKEETIKASAVLFFSEPSTRTRLSFEKAARELGIETYLVSGSESSTVKGESFFDTLKTFEGLGFDYVVFRVPFVFFPYKEIVKSLNLRLVNAGDGTHQHPSQGLIDFFTIKEHFGEVKDLRVLYVGDIKHSRVFRSGAPLLNMFGAKIGVCGPKTLIPRDVEVFKVDVFDDVDKGIDWADVVIWLRLQKERQKENYIPSESSYFKQFGLTKERFEKVKLYMHPGPVNRNVDIDHELVYTEKSLIQEQVKNGIPVRKAIYKFLWT 291
               SCOP domains d4bjhb1 B:1-142 automated matches                                                                                                             d4bjhb2 B:143-291 automated matches                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh........eeeeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhh.hhhhhhhhhhhh...eeeeee......hhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh..eeeee.hhhhh..hhhhh.eeee.hhhhhhhhh.eeee...hhhhh......hhhhhhhhhh.hhhhhh....ee.....................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------CARBAMOY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bjh B   1 MRSLISSLDLTREEVEEILKYAKEFKEGKEETIKASAVLFFSEPSTRTRLSFEKAARELGIETYLVSGSESSTVKGESFFDTLKTFEGLGFDYVVFRVPFVFFPYKEIVKSLNLRLVNAGDGTHQHPSQGLIDFFTIKEHFGEVKDLRVLYVGDIKHSRVFRSGAPLLNMFGAKIGVCGPKTLIPRDVEVFKVDVFDDVDKGIDWADVVIWLRLQKERQKENYIPSESSYFKQFGLTKERFEKVKLYMHPGPVNRNVDIDHELVYTEKSLIQEQVKNGIPVRKAIYKFLWT 291
                                    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
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYRC_AQUAE | O66990)
molecular function
    GO:0004151    dihydroorotase activity    Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0016812    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Chain B   (PYRB_AQUAE | O66726)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0004070    aspartate carbamoyltransferase activity    Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0009220    pyrimidine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
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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  4bjh
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  PYRB_AQUAE | O66726
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  PYRC_AQUAE | O66990
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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
  PYRB_AQUAE | O66726
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PYRC_AQUAE | O66990
    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
        PYRB_AQUAE | O66726: 3d6n
        PYRC_AQUAE | O66990: 1xrf 1xrt 3d6n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BJH)