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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KLUYVEROMYCES LACTIS UREA CARBOXYLASE
 
Authors :  C. Fan, S. Xiang
Date :  29 Dec 11  (Deposition) - 01 Feb 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Carboxylase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Fan, C. Y. Chou, L. Tong, S. Xiang
Crystal Structure Of Urea Carboxylase Provides Insights Int The Carboxyltransfer Reaction
J. Biol. Chem. V. 287 9389 2012
PubMed-ID: 22277658  |  Reference-DOI: 10.1074/JBC.M111.319475

(-) Compounds

Molecule 1 - KLLA0E08119P
    Chains: A
    EC Number: 6.3.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 617-1829
    Gene: KLLA0E08119G
    Organism Common: YEAST
    Organism Scientific: KLUYVEROMYCES LACTIS
    Organism Taxid: 284590
    Strain: NRRL Y-1140
    Synonym: UREA CARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1BTI1Ligand/Ion5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
2GOL7Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4URE1Ligand/IonUREA

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:1324 , ASN A:1330 , THR A:1332 , PRO A:1344 , GLY A:1347 , GLY A:1348 , PHE A:1349 , SER A:1609 , PRO A:1634 , LYS A:1795 , URE A:1902 , HOH A:2008 , HOH A:2352BINDING SITE FOR RESIDUE BTI A 1901
02AC2SOFTWAREASP A:1584 , CYS A:1626 , TYR A:1628 , GLY A:1635 , GLY A:1636 , TYR A:1637 , BTI A:1901 , HOH A:2002BINDING SITE FOR RESIDUE URE A 1902
03AC3SOFTWAREGLN A:976 , ASP A:1648 , LYS A:1649 , LEU A:1650 , ILE A:1652 , ASP A:1687 , HOH A:2010BINDING SITE FOR RESIDUE GOL A 1903
04AC4SOFTWARELYS A:858 , ARG A:914 , GLN A:916 , VAL A:917 , GLU A:918 , ARG A:960 , HOH A:2261BINDING SITE FOR RESIDUE GOL A 1904
05AC5SOFTWAREPRO A:702 , SER A:708 , PHE A:724 , VAL A:725 , GLY A:726 , PRO A:727 , CYS A:891 , ALA A:892 , ALA A:913 , ARG A:914 , LEU A:915 , MET A:934BINDING SITE FOR RESIDUE GOL A 1905
06AC6SOFTWAREARG A:854 , GLN A:857 , VAL A:859 , TYR A:962 , GLU A:964 , HOH A:2124 , HOH A:2194BINDING SITE FOR RESIDUE GOL A 1906
07AC7SOFTWAREHIS A:1287 , ASN A:1289 , ARG A:1296 , GLU A:1335 , PRO A:1608 , SER A:1609 , HOH A:2088 , HOH A:2100BINDING SITE FOR RESIDUE GOL A 1907
08AC8SOFTWAREASN A:1079 , THR A:1126 , ARG A:1180 , MET A:1794 , HOH A:2050 , HOH A:2082BINDING SITE FOR RESIDUE GOL A 1908
09AC9SOFTWAREPRO A:974 , ASN A:1210 , ARG A:1212BINDING SITE FOR RESIDUE GOL A 1909
10BC1SOFTWAREGLU A:1357 , ARG A:1383 , ASP A:1438 , HOH A:2301BINDING SITE FOR RESIDUE NA A 1910

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VA7)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:863 -Pro A:864
2Tyr A:1085 -Pro A:1086
3Gly A:1263 -Pro A:1264
4Leu A:1550 -Pro A:1551
5Asp A:1584 -Val A:1585
6Asn A:1607 -Pro A:1608

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VA7)

(-) Exons   (0, 0)

(no "Exon" information available for 3VA7)

(-) Sequences/Alignments

Asymmetric/Biological 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:1130
 aligned with Q6CP22_KLULA | Q6CP22 from UniProtKB/TrEMBL  Length:1829

    Alignment length:1209
                                   630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      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      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710      1720      1730      1740      1750      1760      1770      1780      1790      1800      1810      1820         
        Q6CP22_KLULA    621 KKPFETVLIANRGEIAVRIMKTLKRMGIKSVAVYSDPDKYSQHVTDADFSVALHGRTAAETYLDIDKIINAAKKTGAQAIIPGYGFLSENADFSDRCSQENIVFVGPSGDAIRKLGLKHSAREIAERAKVPLVPGSGLIKDAKEAKEVAKKLEYPVMVKSTAGGGGIGLQKVDSEDDIERVFETVQHQGKSYFGDAGVFMERFVNNARHVEIQMMGDGFGKAIAIGERDCSLQRRNQKVIEETPAPNLPEATRAKMRAASERLGSLLKYKCAGTVEFIYDEQRDEFYFLEVNARLQVEHPITEMVTGLDLVEWMLRIAANDSPDFDNTKIEVSGASIEARLYAENPVKDFRPSPGQLTSVSFPSWARVDTWVKKGTNVSAEYDPTLAKIIVHGKDRNDAIMKLNQALNETAVYGCITNIDYLRSIASSKMFKEAKVATKVLDSFDYKPCAFEVLAPGANTSVQDYPGRTGYWRIGVPPSGPMDSYSFRLANRVVGNNSKSPALEITLNGPKLLFHTETVIAVSGGTVSCTLNDAQIAQNEPIEVKRGDILSVGKVTVGCRAYLSIRGGIDVPEYLGSRSTFAMGNMGGYNGRILKLGDVLFLNQPELSVSSLPAPDFEPQAAPKSLLPTLSTNKDWKIGVTCGPHGSIDLFKEEYIEQFFNDKWKVHYNSNRFGVRLIGPKPKWARSDGGEAGLHPSNAHDYVYSLGAINFTGDEPVIITCDGPSLGGFVCQAVVAEAELWKVGQLTPGDTIQFVPLSYGVARQLKESQDKSIDNFEEGSLLELSDDKILPKYENPILAVLPKKSDLSPKVTYRQAGDRYILVEYGELEFDLNICYRINRLIHQVERHQTVGIVEMSQGVRSVLIEFDGSKINQKALLKCLIAYESEIQFDKNWNVKSKIFKLPMAFEDSKTLDCVTRYRETIRSEAPWLPNNVDFIADVNDIDRNDVKNMLYSAKFMVLGLGDVFLGSPCAVPLDPRHRYLGTKYNPSRTYTARGVVGIGGMYMCIYNAEGSPGGYQLVGRTITAWDKLVIGDHPIDHPWLLTPFDQVEFYPVTEEELEVIIEDNDNGKFKIDVEESIFDHKEYLAWINENIDSIVAFQEAQGGEKADEFARLIQVANAELKKSGDDKPQDVEEYPDDAELLYSEYTGRFWKPVAAVGDHVEAGDGVIIIEAMKTEMVVGATKSGKVYKILHKNGDMVEAGDLVAVIV 1829
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhh.eeee...........hhhhhhhhhhhh...eee...hhhhhhhhhhhhhhh...ee...hhhhhhhhhh.hhhhhhhhhh......-----------------------------------------------------------------------..eeeeeeeeee....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh....hhhhh......eeeeeeee.ee.....ee..ee..eee.....eeee......ee......eeeeeeeee.hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhh....hhhhhh.....eeeeee.....eee...................hhhhhhhhhhhh.......eeeee....eeee...eeeeeeeeeeeeee..ee......eee....eeeeeeeeeeeeeeeee...............hhhhh.............eee.....................hhhhh.......eeeeeeee.........hhhhhhhhhhh.eeeeeeee..eeeee..........hhhhh....eeeeee....eeeee..eeeee......eeee.eeeee...hhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhh........hhhhh.......eeeee.........eeeee....eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee...eeeeee.....hhhhhhhhhhhhhh........eeeeeeeeeeeee.hhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhh...eeeeee.......eeeee.hhhhh................eeeee..eeee..........eeeee.........................eeeeeeehhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.........--------.......eeee....eeeeee......ee....eeeeeee..eeeeee....eeeeee......ee....eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3va7 A  621 KKPFETVLIANRGEIAVRIMKTLKRMGIKSVAVYSDPDKYSQHVTDADFSVALHGRTAAETYLDIDKIINAAKKTGAQAIIPGYGFLSENADFSDRCSQENIVFVGPSGDAIRKLGLKHSAREIAERAKVPLVP-----------------------------------------------------------------------NARHVEIQMMGDGFGKAIAIGERDCSLQRRNQKVIEETPAPNLPEATRAKMRAASERLGSLLKYKCAGTVEFIYDEQRDEFYFLEVNARLQVEHPITEMVTGLDLVEWMLRIAANDSPDFDNTKIEVSGASIEARLYAENPVKDFRPSPGQLTSVSFPSWARVDTWVKKGTNVSAEYDPTLAKIIVHGKDRNDAIMKLNQALNETAVYGCITNIDYLRSIASSKMFKEAKVATKVLDSFDYKPCAFEVLAPGANTSVQDYPGRTGYWRIGVPPSGPMDSYSFRLANRVVGNNSKSPALEITLNGPKLLFHTETVIAVSGGTVSCTLNDAQIAQNEPIEVKRGDILSVGKVTVGCRAYLSIRGGIDVPEYLGSRSTFAMGNMGGYNGRILKLGDVLFLNQPELSVSSLPAPDFEPQAAPKSLLPTLSTNKDWKIGVTCGPHGSIDLFKEEYIEQFFNDKWKVHYNSNRFGVRLIGPKPKWARSDGGEAGLHPSNAHDYVYSLGAINFTGDEPVIITCDGPSLGGFVCQAVVAEAELWKVGQLTPGDTIQFVPLSYGVARQLKESQDKSIDNFEEGSLLELSDDKILPKYENPILAVLPKKSDLSPKVTYRQAGDRYILVEYGELEFDLNICYRINRLIHQVERHQTVGIVEMSQGVRSVLIEFDGSKINQKALLKCLIAYESEIQFDKNWNVKSKIFKLPMAFEDSKTLDCVTRYRETIRSEAPWLPNNVDFIADVNDIDRNDVKNMLYSAKFMVLGLGDVFLGSPCAVPLDPRHRYLGTKYNPSRTYTARGVVGIGGMYMCIYNAEGSPGGYQLVGRTITAWDKLVIGDHPIDHPWLLTPFDQVEFYPVTEEELEVIIEDNDNGKFKIDVEESIFDHKEYLAWINENIDSIVAFQEAQGGEKADEFARLIQVANAELKKS--------EEYPDDAELLYSEYTGRFWKPVAAVGDHVEAGDGVIIIEAMKTEMVVGATKSGKVYKILHKNGDMVEAGDLVAVIV 1829
                                   630       640       650       660       670       680       690       700       710       720       730       740       750   |     -         -         -         -         -         -         -     | 830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      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      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710      1720      1730      1740    |    -   |  1760      1770      1780      1790      1800      1810      1820         
                                                                                                                                                               754                                                                     826                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   1745     1754
   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 3VA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VA7)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6CP22_KLULA | Q6CP22)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004039    allophanate hydrolase activity    Catalysis of the reaction: H(2)O + 3 H(+) + urea-1-carboxylate = 2 CO(2) + 2 NH(4)(+).
    GO:0004075    biotin carboxylase activity    Catalysis of the reaction: ATP + biotin-carboxyl-carrier protein + CO2 = ADP + phosphate + carboxybiotin-carboxyl-carrier protein.
    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: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:0004847    urea carboxylase activity    Catalysis of the reaction: ATP + bicarbonate + urea = ADP + 2 H(+) + phosphate + urea-1-carboxylate.
biological process
    GO:0043419    urea catabolic process    The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.
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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  3va7
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 Related Entries

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

UniProtKB/TrEMBL
        Q6CP22_KLULA | Q6CP22: 4iss 4ist 5i8i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VA7)