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P83772

- CRNA_PSEPU

UniProt

P83772 - CRNA_PSEPU

Protein

Creatinine amidohydrolase

Gene

crnA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 41 (01 Oct 2014)
      Sequence version 1 (15 Mar 2004)
      Previous versions | rss
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    Functioni

    Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.1 Publication

    Catalytic activityi

    Creatinine + H2O = creatine.2 Publications

    Cofactori

    Binds 2 Zn2+ ions per subunit. The Zn2+ in the metal 1 binding site can be replaced with Mn2+; however, the second zinc in metal binding site 2 is much more tightly bound and can not be replaced. The enzyme with one zinc and one manganese ion is more active than that with two zinc ions.2 Publications

    Enzyme regulationi

    Is markedly inactivated in vitro by heavy metal ions, N-bromosuccinimide, ethoxyformic anhydride, and dye-sensitized photooxidation.1 Publication

    Kineticsi

    1. KM=26 mM for creatinine2 Publications
    2. KM=130 mM for creatine2 Publications
    3. KM=200 mM for glycocyamidine2 Publications

    Vmax=390 µmol/min/mg enzyme for the forward reaction (creatine formation)2 Publications

    Vmax=1510 µmol/min/mg enzyme for the reverse reaction (creatinine formation)2 Publications

    Vmax=3.7 µmol/min/mg enzyme with glycocyamidine as substrate2 Publications

    pH dependencei

    Optimum pH is 7-9 for the forward and reverse reactions.1 Publication

    Temperature dependencei

    Retains 75% of the activity after incubation at 75 degrees Celsius for 30 minutes.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi34 – 341Zinc or manganese 12 Publications
    Metal bindingi36 – 361Zinc 2; via tele nitrogen2 Publications
    Metal bindingi45 – 451Zinc 22 Publications
    Metal bindingi45 – 451Zinc or manganese 12 Publications
    Binding sitei78 – 781Substrate; via carbonyl oxygen
    Metal bindingi120 – 1201Zinc or manganese 1; via pros nitrogen2 Publications
    Binding sitei121 – 1211Substrate; via amide nitrogen
    Sitei122 – 1221Coordinates a catalytic water molecule
    Metal bindingi183 – 1831Zinc 22 Publications

    GO - Molecular functioni

    1. creatininase activity Source: UniProtKB
    2. manganese ion binding Source: UniProtKB
    3. zinc ion binding Source: UniProtKB

    GO - Biological processi

    1. creatine biosynthetic process Source: UniProtKB
    2. creatinine catabolic process Source: UniProtKB

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Manganese, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-10962.
    UniPathwayiUPA00274.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Creatinine amidohydrolase (EC:3.5.2.10)
    Alternative name(s):
    Creatininase
    Gene namesi
    Name:crnA
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi121 – 1211Y → A: 30-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi122 – 1221E → Q: 700-fold decrease in catalytic efficiency. No ion in metal binding site 1. 1 Publication
    Mutagenesisi154 – 1541W → A: Loss of activity. 1 Publication
    Mutagenesisi154 – 1541W → F: 340-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi174 – 1741W → A: Nearly no activity. 1 Publication
    Mutagenesisi174 – 1741W → F: 2-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi178 – 1781H → A: Loss of activity.
    Mutagenesisi183 – 1831E → Q: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 260259Creatinine amidohydrolasePRO_0000406934Add
    BLAST

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.3 Publications

    Structurei

    Secondary structure

    1
    260
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 93
    Helixi12 – 209
    Beta strandi26 – 305
    Beta strandi38 – 403
    Helixi44 – 6017
    Helixi76 – 794
    Beta strandi84 – 863
    Helixi92 – 10918
    Beta strandi113 – 1186
    Helixi121 – 1233
    Helixi124 – 14017
    Beta strandi147 – 1526
    Helixi153 – 1564
    Helixi160 – 1667
    Helixi174 – 1763
    Beta strandi178 – 1803
    Helixi181 – 19010
    Helixi192 – 1943
    Helixi197 – 1993
    Beta strandi210 – 2156
    Helixi218 – 2203
    Helixi235 – 25622

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J2TX-ray1.80A/B/C/D/E/F1-260[»]
    1J2UX-ray1.85A/B/C/D/E/F1-260[»]
    1Q3KX-ray2.10A/B/C/D/E/F2-260[»]
    1V7ZX-ray1.60A/B/C/D/E/F1-260[»]
    3A6DX-ray1.90A/B/C/D/E/F1-260[»]
    3A6EX-ray2.00A/B/C/D/E/F1-260[»]
    3A6FX-ray1.78A/B/C/D/E/F1-260[»]
    3A6GX-ray2.00A/B/C/D/E/F1-260[»]
    3A6HX-ray2.00A/B/C/D/E/F1-260[»]
    3A6JX-ray2.00A/B/C/D/E/F1-260[»]
    3A6KX-ray2.20A/B/C/D/E/F1-260[»]
    3A6LX-ray2.00A/B/C/D/E/F1-260[»]
    ProteinModelPortaliP83772.
    SMRiP83772. Positions 3-259.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP83772.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni174 – 1785Substrate binding

    Sequence similaritiesi

    Belongs to the creatininase superfamily.Curated

    Family and domain databases

    Gene3Di3.40.50.10310. 1 hit.
    InterProiIPR024087. Creatininase-like_dom.
    IPR003785. Creatininase/forma_Hydrolase.
    [Graphical view]
    PfamiPF02633. Creatininase. 1 hit.
    [Graphical view]
    SUPFAMiSSF102215. SSF102215. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P83772-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKSVFVGEL TWKEYEARVA AGDCVLMLPV GALEQHGHHM CMNVDVLLPT    50
    AVCKRVAERI GALVMPGLQY GYKSQQKSGG GNHFPGTTSL DGATLTGTVQ 100
    DIIRELARHG ARRLVLMNGH YENSMFIVEG IDLALRELRY AGIQDFKVVV 150
    LSYWDFVKDP AVIQQLYPEG FLGWDIEHGG VFETSLMLAL YPDLVDLDRV 200
    VDHPPATFPP YDVFPVDPAR TPAPGTLSSA KTASREKGEL ILEVCVQGIA 250
    DAIREEFPPT 260
    Length:260
    Mass (Da):28,569
    Last modified:March 15, 2004 - v1
    Checksum:iE530A7513F57A762
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D45424 Genomic DNA. Translation: BAA08265.1.
    PIRiT48846.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D45424 Genomic DNA. Translation: BAA08265.1 .
    PIRi T48846.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1J2T X-ray 1.80 A/B/C/D/E/F 1-260 [» ]
    1J2U X-ray 1.85 A/B/C/D/E/F 1-260 [» ]
    1Q3K X-ray 2.10 A/B/C/D/E/F 2-260 [» ]
    1V7Z X-ray 1.60 A/B/C/D/E/F 1-260 [» ]
    3A6D X-ray 1.90 A/B/C/D/E/F 1-260 [» ]
    3A6E X-ray 2.00 A/B/C/D/E/F 1-260 [» ]
    3A6F X-ray 1.78 A/B/C/D/E/F 1-260 [» ]
    3A6G X-ray 2.00 A/B/C/D/E/F 1-260 [» ]
    3A6H X-ray 2.00 A/B/C/D/E/F 1-260 [» ]
    3A6J X-ray 2.00 A/B/C/D/E/F 1-260 [» ]
    3A6K X-ray 2.20 A/B/C/D/E/F 1-260 [» ]
    3A6L X-ray 2.00 A/B/C/D/E/F 1-260 [» ]
    ProteinModelPortali P83772.
    SMRi P83772. Positions 3-259.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00274 .
    BioCyci MetaCyc:MONOMER-10962.

    Miscellaneous databases

    EvolutionaryTracei P83772.

    Family and domain databases

    Gene3Di 3.40.50.10310. 1 hit.
    InterProi IPR024087. Creatininase-like_dom.
    IPR003785. Creatininase/forma_Hydrolase.
    [Graphical view ]
    Pfami PF02633. Creatininase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF102215. SSF102215. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Cloning of the creatinine amidohydrolase gene from Pseudomonas sp. PS-7."
      Yamamoto K., Oka M., Kikuchi T., Emi S.
      Biosci. Biotechnol. Biochem. 59:1331-1332(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-6.
      Strain: PS-7.
    2. "Creatinine amidohydrolase (creatininase) from Pseudomonas putida. Purification and some properties."
      Rikitake K., Oka I., Ando M., Yoshimoto T., Tsuru D.
      J. Biochem. 86:1109-1117(1979) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
      Strain: C-83.
    3. "Crystal structure of creatininase from Pseudomonas putida: a novel fold and a case of convergent evolution."
      Beuth B., Niefind K., Schomburg D.
      J. Mol. Biol. 332:287-301(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-260 IN COMPLEX WITH ZINC, COFACTOR, SUBUNIT.
    4. "Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism."
      Yoshimoto T., Tanaka N., Kanada N., Inoue T., Nakajima Y., Haratake M., Nakamura K.T., Xu Y., Ito K.
      J. Mol. Biol. 337:399-416(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF APOENZYME AND COMPLEXES WITH CREATINE; ZINC AND MANGANESE, COFACTOR, SUBUNIT, CATALYTIC MECHANISM.
    5. "Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase."
      Yamashita K., Nakajima Y., Matsushita H., Nishiya Y., Yamazawa R., Wu Y.F., Matsubara F., Oyama H., Ito K., Yoshimoto T.
      J. Mol. Biol. 396:1081-1096(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) OF WILD-TYPE IN COMPLEX WITH 1-METHYLGUANIDINE INHIBITOR AND MUTANTS ALA-154; PHE-154; PHE-174 AND GLN-122 IN COMPLEX WITH CREATINE; ZINC AND MANGANESE, CATALYTIC ACTIVITY, KINETIC PARAMETERS, CATALYTIC MECHANISM, MUTAGENESIS OF TYR-121; GLU-122; TRP-154; TRP-174 AND GLU-183.

    Entry informationi

    Entry nameiCRNA_PSEPU
    AccessioniPrimary (citable) accession number: P83772
    Secondary accession number(s): Q52548
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 5, 2011
    Last sequence update: March 15, 2004
    Last modified: October 1, 2014
    This is version 41 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The proposed catalytic mechanism involves two water molecules. The first molecule is a hydroxide ion that is bound as a bridge between the two metal ions and attacks the carbonyl carbon of the substrate. The second water molecule, that is bound to the carboxyl group of Glu-122 and to the metal 1, functions as a proton donor in catalysis.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3