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Creatinine amidohydrolase (EC 3.5.2.10) (Creatininase)

 CRNA_PSEPU              Reviewed;         260 AA.
P83772; Q52548;
05-APR-2011, integrated into UniProtKB/Swiss-Prot.
15-MAR-2004, sequence version 1.
12-SEP-2018, entry version 55.
RecName: Full=Creatinine amidohydrolase;
EC=3.5.2.10;
AltName: Full=Creatininase;
Name=crnA;
Pseudomonas putida (Arthrobacter siderocapsulatus).
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
Pseudomonadaceae; Pseudomonas.
NCBI_TaxID=303;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-6.
STRAIN=PS-7;
PubMed=7670196; DOI=10.1271/bbb.59.1331;
Yamamoto K., Oka M., Kikuchi T., Emi S.;
"Cloning of the creatinine amidohydrolase gene from Pseudomonas sp.
PS-7.";
Biosci. Biotechnol. Biochem. 59:1331-1332(1995).
[2]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY,
BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY REGULATION.
STRAIN=C-83;
PubMed=500580;
Rikitake K., Oka I., Ando M., Yoshimoto T., Tsuru D.;
"Creatinine amidohydrolase (creatininase) from Pseudomonas putida.
Purification and some properties.";
J. Biochem. 86:1109-1117(1979).
[3]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-260 IN COMPLEX WITH ZINC,
COFACTOR, AND SUBUNIT.
PubMed=12946365; DOI=10.1016/S0022-2836(03)00860-X;
Beuth B., Niefind K., Schomburg D.;
"Crystal structure of creatininase from Pseudomonas putida: a novel
fold and a case of convergent evolution.";
J. Mol. Biol. 332:287-301(2003).
[4]
X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF APOENZYME AND COMPLEXES WITH
CREATINE; ZINC AND MANGANESE, COFACTOR, SUBUNIT, AND CATALYTIC
MECHANISM.
PubMed=15003455; DOI=10.1016/j.jmb.2004.01.022;
Yoshimoto T., Tanaka N., Kanada N., Inoue T., Nakajima Y.,
Haratake M., Nakamura K.T., Xu Y., Ito K.;
"Crystal structures of creatininase reveal the substrate binding site
and provide an insight into the catalytic mechanism.";
J. Mol. Biol. 337:399-416(2004).
[5]
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, AND MUTAGENESIS OF
TYR-121; GLU-122; TRP-154; TRP-174 AND GLU-183.
PubMed=20043918; DOI=10.1016/j.jmb.2009.12.045;
Yamashita K., Nakajima Y., Matsushita H., Nishiya Y., Yamazawa R.,
Wu Y.F., Matsubara F., Oyama H., Ito K., Yoshimoto T.;
"Substitution of Glu122 by glutamine revealed the function of the
second water molecule as a proton donor in the binuclear metal enzyme
creatininase.";
J. Mol. Biol. 396:1081-1096(2010).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:500580}.
-!- CATALYTIC ACTIVITY: Creatinine + H(2)O = creatine.
{ECO:0000269|PubMed:20043918, ECO:0000269|PubMed:500580}.
-!- COFACTOR:
Note=Binds 2 Zn(2+) ions per subunit. The Zn(2+) in the metal 1
binding site can be replaced with Mn(2+); however, the second zinc
in metal binding site 2 is much more tightly bound and cannot be
replaced. The enzyme with one zinc and one manganese ion is more
active than that with two zinc ions. {ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:15003455};
-!- ACTIVITY REGULATION: Is markedly inactivated in vitro by heavy
metal ions, N-bromosuccinimide, ethoxyformic anhydride, and dye-
sensitized photooxidation. {ECO:0000269|PubMed:500580}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=26 mM for creatinine {ECO:0000269|PubMed:20043918,
ECO:0000269|PubMed:500580};
KM=130 mM for creatine {ECO:0000269|PubMed:20043918,
ECO:0000269|PubMed:500580};
KM=200 mM for glycocyamidine {ECO:0000269|PubMed:20043918,
ECO:0000269|PubMed:500580};
Vmax=390 umol/min/mg enzyme for the forward reaction (creatine
formation) {ECO:0000269|PubMed:20043918,
ECO:0000269|PubMed:500580};
Vmax=1510 umol/min/mg enzyme for the reverse reaction
(creatinine formation) {ECO:0000269|PubMed:20043918,
ECO:0000269|PubMed:500580};
Vmax=3.7 umol/min/mg enzyme with glycocyamidine as substrate
{ECO:0000269|PubMed:20043918, ECO:0000269|PubMed:500580};
pH dependence:
Optimum pH is 7-9 for the forward and reverse reactions.
{ECO:0000269|PubMed:500580};
Temperature dependence:
Retains 75% of the activity after incubation at 75 degrees
Celsius for 30 minutes. {ECO:0000269|PubMed:500580};
-!- PATHWAY: Amine and polyamine degradation; creatinine degradation.
-!- SUBUNIT: Homohexamer; trimer of dimers.
{ECO:0000269|PubMed:12946365, ECO:0000269|PubMed:15003455,
ECO:0000269|PubMed:20043918}.
-!- 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.
-!- SIMILARITY: Belongs to the creatininase superfamily.
{ECO:0000305}.
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EMBL; D45424; BAA08265.1; -; Genomic_DNA.
PIR; T48846; T48846.
PDB; 1J2T; X-ray; 1.80 A; A/B/C/D/E/F=1-260.
PDB; 1J2U; X-ray; 1.85 A; A/B/C/D/E/F=1-260.
PDB; 1Q3K; X-ray; 2.10 A; A/B/C/D/E/F=2-260.
PDB; 1V7Z; X-ray; 1.60 A; A/B/C/D/E/F=1-260.
PDB; 3A6D; X-ray; 1.90 A; A/B/C/D/E/F=1-260.
PDB; 3A6E; X-ray; 2.00 A; A/B/C/D/E/F=1-260.
PDB; 3A6F; X-ray; 1.78 A; A/B/C/D/E/F=1-260.
PDB; 3A6G; X-ray; 2.00 A; A/B/C/D/E/F=1-260.
PDB; 3A6H; X-ray; 2.00 A; A/B/C/D/E/F=1-260.
PDB; 3A6J; X-ray; 2.00 A; A/B/C/D/E/F=1-260.
PDB; 3A6K; X-ray; 2.20 A; A/B/C/D/E/F=1-260.
PDB; 3A6L; X-ray; 2.00 A; A/B/C/D/E/F=1-260.
PDBsum; 1J2T; -.
PDBsum; 1J2U; -.
PDBsum; 1Q3K; -.
PDBsum; 1V7Z; -.
PDBsum; 3A6D; -.
PDBsum; 3A6E; -.
PDBsum; 3A6F; -.
PDBsum; 3A6G; -.
PDBsum; 3A6H; -.
PDBsum; 3A6J; -.
PDBsum; 3A6K; -.
PDBsum; 3A6L; -.
ProteinModelPortal; P83772; -.
SMR; P83772; -.
BioCyc; MetaCyc:MONOMER-10962; -.
BRENDA; 3.5.2.10; 5092.
SABIO-RK; P83772; -.
UniPathway; UPA00274; -.
EvolutionaryTrace; P83772; -.
GO; GO:0047789; F:creatininase activity; IDA:UniProtKB.
GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
GO; GO:0006601; P:creatine biosynthetic process; IDA:UniProtKB.
GO; GO:0006602; P:creatinine catabolic process; IDA:UniProtKB.
Gene3D; 3.40.50.10310; -; 1.
InterPro; IPR031034; Creatininase.
InterPro; IPR024087; Creatininase-like_sf.
InterPro; IPR003785; Creatininase/forma_Hydrolase.
PANTHER; PTHR35005; PTHR35005; 1.
Pfam; PF02633; Creatininase; 1.
SUPFAM; SSF102215; SSF102215; 1.
TIGRFAMs; TIGR04448; creatininase; 1.
1: Evidence at protein level;
3D-structure; Direct protein sequencing; Hydrolase; Manganese;
Metal-binding; Zinc.
INIT_MET 1 1 Removed. {ECO:0000305|PubMed:7670196}.
CHAIN 2 260 Creatinine amidohydrolase.
/FTId=PRO_0000406934.
REGION 174 178 Substrate binding.
METAL 34 34 Zinc or manganese 1.
{ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:20043918}.
METAL 36 36 Zinc 2; via tele nitrogen.
{ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:20043918}.
METAL 45 45 Zinc 2. {ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:20043918}.
METAL 45 45 Zinc or manganese 1.
{ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:20043918}.
METAL 120 120 Zinc or manganese 1; via pros nitrogen.
{ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:20043918}.
METAL 183 183 Zinc 2. {ECO:0000269|PubMed:12946365,
ECO:0000269|PubMed:20043918}.
BINDING 78 78 Substrate; via carbonyl oxygen.
BINDING 121 121 Substrate; via amide nitrogen.
SITE 122 122 Coordinates a catalytic water molecule.
MUTAGEN 121 121 Y->A: 30-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:20043918}.
MUTAGEN 122 122 E->Q: 700-fold decrease in catalytic
efficiency. No ion in metal binding site
1. {ECO:0000269|PubMed:20043918}.
MUTAGEN 154 154 W->A: Loss of activity.
{ECO:0000269|PubMed:20043918}.
MUTAGEN 154 154 W->F: 340-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:20043918}.
MUTAGEN 174 174 W->A: Nearly no activity.
{ECO:0000269|PubMed:20043918}.
MUTAGEN 174 174 W->F: 2-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:20043918}.
MUTAGEN 178 178 H->A: Loss of activity.
MUTAGEN 183 183 E->Q: Loss of activity.
{ECO:0000269|PubMed:20043918}.
HELIX 7 9 {ECO:0000244|PDB:1V7Z}.
HELIX 12 20 {ECO:0000244|PDB:1V7Z}.
STRAND 26 30 {ECO:0000244|PDB:1V7Z}.
STRAND 38 40 {ECO:0000244|PDB:1V7Z}.
HELIX 44 60 {ECO:0000244|PDB:1V7Z}.
HELIX 76 79 {ECO:0000244|PDB:1V7Z}.
STRAND 84 86 {ECO:0000244|PDB:1V7Z}.
HELIX 92 109 {ECO:0000244|PDB:1V7Z}.
STRAND 113 118 {ECO:0000244|PDB:1V7Z}.
HELIX 121 123 {ECO:0000244|PDB:1V7Z}.
HELIX 124 140 {ECO:0000244|PDB:1V7Z}.
STRAND 147 152 {ECO:0000244|PDB:1V7Z}.
HELIX 153 156 {ECO:0000244|PDB:1V7Z}.
HELIX 160 166 {ECO:0000244|PDB:1V7Z}.
HELIX 174 176 {ECO:0000244|PDB:3A6F}.
STRAND 178 180 {ECO:0000244|PDB:1V7Z}.
HELIX 181 190 {ECO:0000244|PDB:1V7Z}.
HELIX 192 194 {ECO:0000244|PDB:1V7Z}.
HELIX 197 199 {ECO:0000244|PDB:1V7Z}.
STRAND 210 215 {ECO:0000244|PDB:1V7Z}.
HELIX 218 220 {ECO:0000244|PDB:1V7Z}.
HELIX 235 256 {ECO:0000244|PDB:1V7Z}.
SEQUENCE 260 AA; 28569 MW; E530A7513F57A762 CRC64;
MSKSVFVGEL TWKEYEARVA AGDCVLMLPV GALEQHGHHM CMNVDVLLPT AVCKRVAERI
GALVMPGLQY GYKSQQKSGG GNHFPGTTSL DGATLTGTVQ DIIRELARHG ARRLVLMNGH
YENSMFIVEG IDLALRELRY AGIQDFKVVV LSYWDFVKDP AVIQQLYPEG FLGWDIEHGG
VFETSLMLAL YPDLVDLDRV VDHPPATFPP YDVFPVDPAR TPAPGTLSSA KTASREKGEL
ILEVCVQGIA DAIREEFPPT


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