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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD IN APO-FORM OBTAINED RECOMBINANTLY FROM E. COLI.
 
Authors :  S. Ramon-Maiques, N. Lallous, A. Grande-Garcia
Date :  17 Jul 13  (Deposition) - 28 May 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, De Novo Pyrimidine Biosynthesis, Amidohydrolase Superfamily, Metalloenzyme, Zinc Binding, Histidinate Anion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Grande-Garcia, N. Lallous, C. Diaz-Tejada, S. Ramon-Maiques
Structure, Functional Characterization, And Evolution Of The Dihydroorotase Domain Of Human Cad.
Structure V. 22 185 2014
PubMed-ID: 24332717  |  Reference-DOI: 10.1016/J.STR.2013.10.016

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    ChainsA
    EC Number3.4.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPIN-M
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1456-1846
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCAD PROTEIN

 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, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1FMT8Ligand/IonFORMIC ACID
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREZN A:1001 , HIS A:1471 , HIS A:1473 , KCX A:1556 , ASP A:1686 , HOH A:2061BINDING SITE FOR RESIDUE ZN A1000
2AC2SOFTWAREZN A:1000 , KCX A:1556 , HIS A:1590 , HIS A:1614 , HOH A:2061BINDING SITE FOR RESIDUE ZN A1001
3AC3SOFTWAREHIS A:1471 , CYS A:1613 , GLU A:1637 , HOH A:2063BINDING SITE FOR RESIDUE ZN A1002
4AC4SOFTWAREHIS A:1734 , HIS A:1741 , HOH A:2064 , HOH A:2065BINDING SITE FOR RESIDUE ZN A1003
5AC5SOFTWAREPRO A:1586 , ILE A:1587 , ARG A:1608 , SER A:1609 , VAL A:1610 , HIS A:1611 , HOH A:2193 , HOH A:2196BINDING SITE FOR RESIDUE FMT A2822
6AC6SOFTWAREHIS A:1734 , ARG A:1737BINDING SITE FOR RESIDUE FMT A2823
7AC7SOFTWAREARG A:1463 , THR A:1748 , GLN A:1814 , HOH A:2070 , HOH A:2323BINDING SITE FOR RESIDUE FMT A2824
8AC8SOFTWAREHIS A:1473 , ARG A:1475 , ASN A:1505 , HIS A:1690 , PRO A:1702BINDING SITE FOR RESIDUE FMT A2825

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BY3)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:1476 -Pro A:1477
2Arg A:1507 -Pro A:1508
3Arg A:1661 -Pro A:1662

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BY3)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYR1_HUMAN1469-1477  1A:1469-1477
2DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYR1_HUMAN1684-1695  1A:1684-1695
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DIHYDROOROTASE_1PS00482 Dihydroorotase signature 1.PYR1_HUMAN1469-1477  2A:1469-1477
2DIHYDROOROTASE_2PS00483 Dihydroorotase signature 2.PYR1_HUMAN1684-1695  2A:1684-1695

(-) Exons   (0, 0)

(no "Exon" information available for 4BY3)

(-) 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:362
 aligned with PYR1_HUMAN | P27708 from UniProtKB/Swiss-Prot  Length:2225

    Alignment length:362
                                  1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659      1669      1679      1689      1699      1709      1719      1729      1739      1749      1759      1769      1779      1789      1799      1809      1819  
          PYR1_HUMAN   1460 KLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDAPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLKLYLNETFSELRLDSVVQWMEHFETWPSHLPIVAHAEQQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLP 1821
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee.ee...........hhhhh..eeee...........hhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.ee.......hhhhhh.........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee.........hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------DIHYDROOR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4by3 A 1460 KLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDAPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLkLYLNETFSELRLDSVVQWMEHFETWPSHLPIVAHAEQQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLP 1821
                                  1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659      1669      1679      1689      1699      1709      1719      1729      1739      1749      1759      1769      1779      1789      1799      1809      1819  
                                                                                                                         1556-KCX                                                                                                                                                                                                                                                                     

   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  (0, 0)

(no "SCOP Domain" information available for 4BY3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BY3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BY3)

(-) Gene Ontology  (56, 56)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYR1_HUMAN | P27708)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0070335    aspartate binding    Interacting selectively and non-covalently with aspartate, the alpha-amino-acid anion of 2-aminobutanedioic acid that has formula C4H5NO4.
    GO:0004070    aspartate carbamoyltransferase activity    Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
    GO:0004087    carbamoyl-phosphate synthase (ammonia) activity    Catalysis of the reaction: 2 ATP + CO(2) + H(2)O + NH(4)(+) = 2 ADP + carbamoyl phosphate + 5 H(+) + phosphate.
    GO:0004088    carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity    Catalysis of the reaction: 2 ATP + L-glutamine + CO2 + H2O = 2 ADP + phosphate + glutamate + carbamoyl 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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004151    dihydroorotase activity    Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    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.
    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: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:0006228    UTP biosynthetic process    The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    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:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071364    cellular response to epidermal growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus.
    GO:0017144    drug metabolic process    The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0046134    pyrimidine nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    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:0014075    response to amine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    GO:0031000    response to caffeine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
    GO:0051414    response to cortisol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cortisol stimulus. Cortisol is the major natural glucocorticoid synthesized in the zona fasciculata of the adrenal cortex; it affects the metabolism of glucose, protein, and fats and has appreciable mineralocorticoid activity. It also regulates the immune system and affects many other functions.
    GO:0033574    response to testosterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYR1_HUMAN | P277084c6b 4c6c 4c6d 4c6e 4c6f 4c6i 4c6j 4c6k 4c6l 4c6m 4c6n 4c6o 4c6p 4c6q 5g1n 5g1o 5g1p

(-) Related Entries Specified in the PDB File

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