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Title :   CRYSTAL STRUCTURE OF NITRILE HYDRATASE MUTANT S113A COMPLEXED WITH TRIMETHYLACETONITRILE

Authors :   Y. Yamanaka, K. Hashimoto, A. Ohtaki, K. Noguchi, M. Yohda, M. Odaka

Date :   06 Oct 09 (Deposition) - 14 Apr 10 (Release) - 22 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.11

Chains :   Asym./Biol. Unit : A,B

Keywords :   Nitrile Hydratase, Fe, Iron, Lyase, Metal-Binding, Oxidation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Yamanaka, K. Hashimoto, A. Ohtaki, K. Noguchi, M. Yohda, M. Odaka
Kinetic And Structural Studies On Roles Of The Serine Ligan And A Strictly Conserved Tyrosine Residue In Nitrile Hydratase
J. Biol. Inorg. Chem. V. 15 655 2010
PubMed-ID: 20221653 | Reference-DOI: 10.1007/S00775-010-0632-3

Molecule 1 - NITRILE HYDRATASE SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	4.2.1.84
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRCN103
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Strain	:	N-771
	Synonym	:	NITRILE HYDRATASE ALPHA-SUBUNIT, NITRILASE, NHASE

Molecule 2 - NITRILE HYDRATASE SUBUNIT BETA
	Chains	:	B
	EC Number	:	4.2.1.84
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHSGB
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Strain	:	N-771
	Synonym	:	NITRILE HYDRATASE BETA-SUBUNIT, NITRILASE, NHASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 8)

No.	Name	Count	Type	Full Name
1	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	FE	1	Ligand/Ion	FE (III) ION
4	MG	3	Ligand/Ion	MAGNESIUM ION
5	NO	1	Ligand/Ion	NITRIC OXIDE
6	TAN	1	Ligand/Ion	2,2-DIMETHYLPROPANENITRILE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:109 , CSD A:112 , ALA A:113 , CSO A:114 , NO A:207	BINDING SITE FOR RESIDUE FE A 301
2	AC2	SOFTWARE	CSD A:112 , ALA A:113 , CSO A:114 , HOH A:239 , FE A:301 , TAN B:213	BINDING SITE FOR RESIDUE NO A 207
3	AC3	SOFTWARE	HOH B:324 , HOH B:432 , HOH B:433 , HOH B:434 , HOH B:435 , HOH B:436	BINDING SITE FOR RESIDUE MG B 302
4	AC4	SOFTWARE	HOH B:425 , HOH B:426 , HOH B:427 , HOH B:428 , HOH B:429 , HOH B:430	BINDING SITE FOR RESIDUE MG B 303
5	AC5	SOFTWARE	HOH B:381 , HOH B:386 , HOH B:388 , HOH B:389 , HOH B:401 , HOH B:405	BINDING SITE FOR RESIDUE MG B 304
6	AC6	SOFTWARE	NO A:207 , TYR B:37 , MET B:40 , ARG B:56 , TYR B:72 , TYR B:76	BINDING SITE FOR RESIDUE TAN B 213

(no "SS Bond" information available for 3A8G)

(no "Cis Peptide Bond" information available for 3A8G)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NHAB_RHOER_001 *	M	40	V	NHAB_RHOER	---	---	B	M	40	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3A8G)

(no "Exon" information available for 3A8G)

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:197
 aligned with NHAA_RHOER | P13448 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:197
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
           NHAA_RHOER    10 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 206
               SCOP domains d3a8ga_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 3a8gA00 A:9-205 Nitrile Hydratase; Chain A                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeeee..........hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8g A   9 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcAcTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 205
                                    18        28        38        48        58        68        78        88        98       108   | | 118       128       138       148       158       168       178       188       198       
                                                                                                                                 112-CSD                                                                                         
                                                                                                                                   114-CSO

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with NHAB_RHOER | P13449 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           NHAB_RHOER     1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
               SCOP domains d3a8gb_ B: Iron-containing nitrile hydratase                                                                                                                                                                         SCOP domains
               CATH domains 3a8gB01 B:1-110  [code=1.10.472.20, no name defined]                                                          3a8gB02 B:111-212  [code=2.30.30.50, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........................eeee...........hhhhh..eeeeeee......hhhhhh..........eeeeeeehhhhhh......eeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8g B   1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

(no "Pfam Domain" information available for 3A8G)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NHAA_RHOER | P13448)

molecular function
	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:0080109	indole-3-acetonitrile nitrile hydratase activity	Catalysis of the reaction: indole-3-acetonitrile + H2O = indole-3-acetamide.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0018822	nitrile hydratase activity	Catalysis of the reaction: an aliphatic amide = a nitrile + H2O.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Chain B (NHAB_RHOER | P13449)

molecular function
	GO:0080109	indole-3-acetonitrile nitrile hydratase activity	Catalysis of the reaction: indole-3-acetonitrile + H2O = indole-3-acetamide.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0018822	nitrile hydratase activity	Catalysis of the reaction: an aliphatic amide = a nitrile + H2O.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3a8g)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (0, 0)

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SCOP Domains (2, 2)

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