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P83772

- CRNA_PSEPU

UniProt

P83772 - CRNA_PSEPU

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Protein

Creatinine amidohydrolase

Gene

crnA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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

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 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
Complete GO annotation...

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 – 93Combined sources
Helixi12 – 209Combined sources
Beta strandi26 – 305Combined sources
Beta strandi38 – 403Combined sources
Helixi44 – 6017Combined sources
Helixi76 – 794Combined sources
Beta strandi84 – 863Combined sources
Helixi92 – 10918Combined sources
Beta strandi113 – 1186Combined sources
Helixi121 – 1233Combined sources
Helixi124 – 14017Combined sources
Beta strandi147 – 1526Combined sources
Helixi153 – 1564Combined sources
Helixi160 – 1667Combined sources
Helixi174 – 1763Combined sources
Beta strandi178 – 1803Combined sources
Helixi181 – 19010Combined sources
Helixi192 – 1943Combined sources
Helixi197 – 1993Combined sources
Beta strandi210 – 2156Combined sources
Helixi218 – 2203Combined sources
Helixi235 – 25622Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MSKSVFVGEL TWKEYEARVA AGDCVLMLPV GALEQHGHHM CMNVDVLLPT
60 70 80 90 100
AVCKRVAERI GALVMPGLQY GYKSQQKSGG GNHFPGTTSL DGATLTGTVQ
110 120 130 140 150
DIIRELARHG ARRLVLMNGH YENSMFIVEG IDLALRELRY AGIQDFKVVV
160 170 180 190 200
LSYWDFVKDP AVIQQLYPEG FLGWDIEHGG VFETSLMLAL YPDLVDLDRV
210 220 230 240 250
VDHPPATFPP YDVFPVDPAR TPAPGTLSSA KTASREKGEL ILEVCVQGIA
260
DAIREEFPPT
Length:260
Mass (Da):28,569
Last modified:March 15, 2004 - v1
Checksum:iE530A7513F57A762
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D45424 Genomic DNA. Translation: BAA08265.1.
PIRiT48846.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D45424 Genomic DNA. Translation: BAA08265.1 .
PIRi T48846.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 42 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