2AHJ - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE

Authors :   S. Nagashima, M. Nakasako, N. Dohmae, M. Tsujimura, K. Takio, M. Odaka, M. Yohda, N. Kamiya, I. Endo

Date :   24 Dec 97 (Deposition) - 27 Jan 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B,C,D  (2x)

Keywords :   Lyase, Photoreactive Enzyme, Nitric Oxide Binding Enzyme, Non-Heme Iron Center, Post-Translational Modification Of Cysteine Residues, Hydratase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Nagashima, M. Nakasako, N. Dohmae, M. Tsujimura, K. Takio, M. Odaka, M. Yohda, N. Kamiya, I. Endo
Novel Non-Heme Iron Center Of Nitrile Hydratase With A Claw Setting Of Oxygen Atoms.
Nat. Struct. Biol. V. 5 347 1998
PubMed-ID: 9586994 | Reference-DOI: 10.1038/NSB0598-347
(for further references see the PDB file header)

Molecule 1 - NITRILE HYDRATASE
	Chains	:	A, C
	EC Number	:	4.2.1.84
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Other Details	:	IN NITROSYLATED STATE (INACTIVE FORM)
	Strain	:	SP. N-771
	Synonym	:	NHASE

Molecule 2 - NITRILE HYDRATASE
	Chains	:	B, D
	EC Number	:	4.2.1.84
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Other Details	:	IN NITROSYLATED STATE (INACTIVE FORM)
	Strain	:	SP. N-771
	Synonym	:	NHASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 15)

No.	Name	Count	Type	Full Name
1	CSD	2	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	DIO	2	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
4	FE	2	Ligand/Ion	FE (III) ION
5	NO	2	Ligand/Ion	NITRIC OXIDE
6	SO4	3	Ligand/Ion	SULFATE ION
7	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 9)

No.	Name	Count	Type	Full Name
1	CSD	2	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	DIO	2	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
4	FE	-1	Ligand/Ion	FE (III) ION
5	NO	-1	Ligand/Ion	NITRIC OXIDE
6	SO4	3	Ligand/Ion	SULFATE ION
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 18)

No.	Name	Count	Type	Full Name
1	CSD	4	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	4	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	DIO	4	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
4	FE	-1	Ligand/Ion	FE (III) ION
5	NO	-1	Ligand/Ion	NITRIC OXIDE
6	SO4	6	Ligand/Ion	SULFATE ION
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:109 , CSD A:112 , SER A:113 , CSO A:114 , NO A:301	BINDING SITE FOR RESIDUE FE A 300
02	AC2	SOFTWARE	HIS B:29 , HIS C:6 , HOH C:394 , GLU D:31	BINDING SITE FOR RESIDUE ZN C 303
03	AC3	SOFTWARE	CYS C:109 , CSD C:112 , SER C:113 , CSO C:114 , NO C:301	BINDING SITE FOR RESIDUE FE C 300
04	AC4	SOFTWARE	HIS A:6 , HOH A:387 , HOH A:460 , GLU B:31 , HIS D:29	BINDING SITE FOR RESIDUE ZN A 303
05	AC5	SOFTWARE	ARG B:107 , GLY D:14 , LYS D:15 , HOH D:461 , HOH D:462 , HOH D:486	BINDING SITE FOR RESIDUE SO4 D 304
06	AC6	SOFTWARE	SER A:182 , GLN A:183 , ARG D:128 , THR D:152 , HOH D:309 , HOH D:414	BINDING SITE FOR RESIDUE SO4 A 305
07	AC7	SOFTWARE	GLY B:14 , LYS B:15 , HOH B:410 , ARG D:107	BINDING SITE FOR RESIDUE SO4 B 306
08	AC8	SOFTWARE	CSD A:112 , SER A:113 , CSO A:114 , FE A:300 , DIO B:302	BINDING SITE FOR RESIDUE NO A 301
09	AC9	SOFTWARE	TRP A:117 , NO A:301 , TYR B:37 , VAL B:52 , ARG B:56 , TYR B:76	BINDING SITE FOR RESIDUE DIO B 302
10	BC1	SOFTWARE	CSD C:112 , SER C:113 , CSO C:114 , FE C:300 , DIO D:302	BINDING SITE FOR RESIDUE NO C 301
11	BC2	SOFTWARE	NO C:301 , TYR D:37 , VAL D:52 , TYR D:76	BINDING SITE FOR RESIDUE DIO D 302
12	CTA	UNKNOWN	CYS A:109 , CSD A:112 , SER A:113 , CSO A:114	NON-HEME IRON CENTER AND CATALYTIC SITE IN CHAIN A
13	CTB	UNKNOWN	CYS C:109 , CSD C:112 , SER C:113 , CSO C:114	NON-HEME IRON CENTER AND CATALYTIC SITE IN CHAIN C

(no "SS Bond" information available for 2AHJ)

(no "Cis Peptide Bond" information available for 2AHJ)

Asymmetric Unit (1, 2)

								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/D	M	40	V
	* ID not provided by source

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

Biological Unit 1 (1, 2)

								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/D	M	40	V
	* ID not provided by source

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

Biological Unit 2 (1, 4)

								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/D	M	40	V
	* ID not provided by source

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

(no "PROSITE Motif" information available for 2AHJ)

(no "Exon" information available for 2AHJ)

Asymmetric 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:194
 aligned with NHAA_RHOER | P13448 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:200
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
           NHAA_RHOER     5 IDHTTENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQV 204
               SCOP domains d2a      hja_ A: Iron-containing nitrile hydratase                                                                                                                                                       SCOP domains
               CATH domains 2ah      jA00 A:4-203 Nitrile Hydratase; Chain A                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------.....hhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhh.........eeeee....eeeeee........hhhh....hhhh.hhhhhh....hhhhhhhh........eeeeee.....eeeee...........hhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahj A   4 IDH------PAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcScTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQV 203
                              |     13        23        33        43        53        63        73        83        93       103       113|      123       133       143       153       163       173       183       193       203
                              6     13                                                                                                112-CSD                                                                                       
                                                                                                                                        114-CSO

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with NHAB_RHOER | P13449 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           NHAB_RHOER     1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPA 211
               SCOP domains d2ahjb_ B: Iron-containing nitrile hydratase                                                                                                                                                                        SCOP domains
               CATH domains 2ahjB01 B:1-110  [code=1.10.472.20, no name defined]                                                          2ahjB02 B:111-211  [code=2.30.30.50, no name defined]                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhh......hhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhh............................eeee............hhh...eeeeeee.......hhhhhh.........eeeeeeehhhhh.......eeeeeeehhheee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahj B   1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPA 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:195
 aligned with NHAA_RHOER | P13448 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:200
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
           NHAA_RHOER     5 IDHTTENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQV 204
               SCOP domains d2a     hjc_ C: Iron-containing nitrile hydratase                                                                                                                                                        SCOP domains
               CATH domains 2ah     jC00 C:4-203 Nitrile Hydratase; Chain A                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-----......hhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhh.........eeeee....eeeeee........hhhh....hhhh.hhhhhhhhh.hhhhhhhh........eeeeee.....eeeee...........hhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahj C   4 IDH-----APAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcScTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQV 203
                              |     13        23        33        43        53        63        73        83        93       103       113|      123       133       143       153       163       173       183       193       203
                              6    12                                                                                                 112-CSD                                                                                       
                                                                                                                                        114-CSO

Chain D 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 d2ahjd_ D: Iron-containing nitrile hydratase                                                                                                                                                                         SCOP domains
               CATH domains 2ahjD01 D:1-110  [code=1.10.472.20, no name defined]                                                          2ahjD02 D:111-212  [code=2.30.30.50, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhh......hhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhh............................eeee............hhh...eeeeeee.......hhhhhh.........eeeeeeehhhhh.......eeeeeeehhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahj D   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 2AHJ)

Asymmetric Unit(hide GO term definitions)

Chain A,C (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,D (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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ahj)

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(no "Related Entries Specified in the PDB File" available for 2AHJ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 15)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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Exons (0, 0)

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