1KRH - JenaLib

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Title :   X-RAY STRUCTURE OF BENZOATE DIOXYGENASE REDUCTASE

Authors :   A. Karlsson, Z. M. Beharry, D. M. Eby, E. D. Coulter, E. L. Niedle, D. M. Ku H. Eklund, S. Ramaswamy

Date :   09 Jan 02 (Deposition) - 15 May 02 (Release) - 01 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Alpha-Beta, Fad-Binding, Ferredoxin, Nadh-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Karlsson, Z. M. Beharry, D. Matthew Eby, E. D. Coulter, E. L. Neidle D. M. Kurtz Jr. , H. Eklund, S. Ramaswamy
X-Ray Crystal Structure Of Benzoate 1, 2-Dioxygenase Reductase From Acinetobacter Sp. Strain Adp1.
J. Mol. Biol. V. 318 261 2002
PubMed-ID: 12051836 | Reference-DOI: 10.1016/S0022-2836(02)00039-6

Molecule 1 - BENZOATE 1,2-DIOXYGENASE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.18.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAC297
	Expression System Strain	:	BL21-CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BENC
	Organism Scientific	:	ACINETOBACTER SP.
	Organism Taxid	:	472

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:210 , ARG A:211 , ASN A:329	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	ARG A:32 , HOH A:655 , HOH A:722 , HOH A:723 , HOH A:725 , ARG B:174 , GLY B:219 , THR B:248 , HOH B:617	BINDING SITE FOR RESIDUE SO4 A 401
3	AC3	SOFTWARE	ARG A:174 , GLY A:219 , THR A:248 , ASP A:252 , HOH A:635 , HOH A:637 , HOH A:721 , HOH A:724 , HOH A:727 , ARG B:32	BINDING SITE FOR RESIDUE SO4 A 402
4	AC4	SOFTWARE	ARG A:284 , THR B:153 , HOH B:602 , HOH B:603	BINDING SITE FOR RESIDUE SO4 B 403
5	AC5	SOFTWARE	LYS B:210 , ARG B:211 , ASN B:329	BINDING SITE FOR RESIDUE SO4 B 404
6	AC6	SOFTWARE	MET A:39 , ASP A:40 , CYS A:41 , ARG A:42 , GLY A:44 , GLU A:45 , CYS A:46 , GLY A:47 , CYS A:49 , CYS A:83	BINDING SITE FOR RESIDUE FES A 500
7	AC7	SOFTWARE	TYR A:144 , ARG A:156 , SER A:157 , TYR A:158 , SER A:159 , VAL A:172 , VAL A:173 , ARG A:174 , GLY A:179 , LYS A:180 , MET A:181 , SER A:182 , THR A:220 , GLU A:333 , PHE A:335 , SER A:336 , ALA A:337 , ASN A:338 , HOH A:528 , HOH A:638 , HOH A:639 , HOH A:719 , HOH A:726 , ARG B:16 , GLN B:34	BINDING SITE FOR RESIDUE FAD A 501
8	AC8	SOFTWARE	MET B:39 , ASP B:40 , CYS B:41 , ARG B:42 , GLY B:44 , GLU B:45 , CYS B:46 , GLY B:47 , CYS B:49 , CYS B:83	BINDING SITE FOR RESIDUE FES B 600
9	AC9	SOFTWARE	ARG A:16 , GLN A:34 , HOH A:507 , HOH A:508 , TYR B:144 , ARG B:156 , SER B:157 , TYR B:158 , SER B:159 , VAL B:172 , VAL B:173 , ARG B:174 , VAL B:176 , GLY B:179 , LYS B:180 , MET B:181 , SER B:182 , THR B:220 , ALA B:223 , GLU B:333 , LYS B:334 , PHE B:335 , SER B:336 , ALA B:337 , ASN B:338 , HOH B:611 , HOH B:627	BINDING SITE FOR RESIDUE FAD B 601

(no "SS Bond" information available for 1KRH)

Asymmetric Unit

No.	Residues
1	Gly A:199	-	Pro A:200
2	Gly B:199	-	Pro B:200

(no "SAP(SNP)/Variant" information available for 1KRH)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	BENC_ACIAD	14-109	2	A:4-99 B:4-99
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	BENC_ACIAD	51-59	2	A:41-49 B:41-49
3	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	BENC_ACIAD	116-217	2	A:106-207 B:106-207

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	BENC_ACIAD	14-109	1	A:4-99 -
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	BENC_ACIAD	51-59	1	A:41-49 -
3	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	BENC_ACIAD	116-217	1	A:106-207 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	BENC_ACIAD	14-109	1	- B:4-99
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	BENC_ACIAD	51-59	1	- B:41-49
3	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	BENC_ACIAD	116-217	1	- B:106-207

(no "Exon" information available for 1KRH)

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:337
 aligned with BENC_ACIAD | P07771 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:337
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
           BENC_ACIAD    12 SNHQVALQFEDGVTRFIRIAQGETLSDAAYRQQINIPMDCREGACGTCRAFCESGNYDMPEDNYIEDALTPEEAQQGYVLACQCRPTSDAVFQIQASSEVCKTKIHHFEGTLARVENLSDSTITFDIQLDDGQPDIHFLAGQYVNVTLPGTTETRSYSFSSQPGNRLTGFVVRNVPQGKMSEYLSVQAKAGDKMSFTGPFGSFYLRDVKRPVLMLAGGTGIAPFLSMLQVLEQKGSEHPVRLVFGVTQDCDLVALEQLDALQQKLPWFEYRTVVAHAESQHERKGYVTGHIEYDWLNGGEVDVYLCGPVPMVEAVRSWLDTQGIQPANFLFEKFSAN 348
               SCOP domains d1krha3 A:2-105 Benzoate dioxygenase reductase, N-terminal domain                                       d1krha1 A:106-205 Benzoate dioxygenase reductase                                                    d1krha2 A:206-338 Benzoate dioxygenase reductase                                                                                      SCOP domains
               CATH domains 1krhA01 A:2-104  [code=3.10.20.30, no name defined]                                                    1krhA02 A:105-201 Translation factors                                                            1krhA03 A:202-335 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                 --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee....hhhhhhhhhh...............eeeeee..ee.hhhhh.....hhhhhhhheee....ee...eeeee....hhhhh...eeeeeeeeeee....eeeeeeee.............eeeee......eeeee........eeeeeee....hhhhhhhhh......eeeeeeee...........eeeeeee.hhhhhhhhhhhhhhhh....eeeeeee.hhhhh.hhhhhhhhhhhh..eeeeeee........ee..hhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhh....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: A:4-99 UniProt: 14-109                                                        ------FAD_FR  PDB: A:106-207 UniProt: 116-217                                                               ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------2FE2S_FER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1krh A   2 SNHQVALQFEDGVTRFICIAQGETLSDAAYRQQINIPMDCREGECGTCRAFCESGNYDMPEDNYIEDALTPEEAQQGYVLACQCRPTSDAVFQIQASSEVCKTKIHHFEGTLARVENLSDSTITFDIQLDDGQPDIHFLAGQYVNVTLPGTTETRSYSFSSQPGNRLTGFVVRNVPQGKMSEYLSVQAKAGDKMSFTGPFGSFYLRDVKRPVLMLAGGTGIAPFLSMLQVLEQKGSEHPVRLVFGVTQDCDLVALEQLDALQQKLPWFEYRTVVAHAESQHERKGYVTGHIEYDWLNGGEVDVYLCGPVPMVEAVRSWLDTQGIQPANFLFEKFSAN 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with BENC_ACIAD | P07771 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:337
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
           BENC_ACIAD    12 SNHQVALQFEDGVTRFIRIAQGETLSDAAYRQQINIPMDCREGACGTCRAFCESGNYDMPEDNYIEDALTPEEAQQGYVLACQCRPTSDAVFQIQASSEVCKTKIHHFEGTLARVENLSDSTITFDIQLDDGQPDIHFLAGQYVNVTLPGTTETRSYSFSSQPGNRLTGFVVRNVPQGKMSEYLSVQAKAGDKMSFTGPFGSFYLRDVKRPVLMLAGGTGIAPFLSMLQVLEQKGSEHPVRLVFGVTQDCDLVALEQLDALQQKLPWFEYRTVVAHAESQHERKGYVTGHIEYDWLNGGEVDVYLCGPVPMVEAVRSWLDTQGIQPANFLFEKFSAN 348
               SCOP domains d1krhb3 B:2-105 Benzoate dioxygenase reductase, N-terminal domain                                       d1krhb1 B:106-205 Benzoate dioxygenase reductase                                                    d1krhb2 B:206-338 Benzoate dioxygenase reductase                                                                                      SCOP domains
               CATH domains 1krhB01 B:2-104  [code=3.10.20.30, no name defined]                                                    1krhB02 B:105-201 Translation factors                                                            1krhB03 B:202-335 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                 --- CATH domains
           Pfam domains (1) -------Fer2-1krhB03 B:9-88                                                             ---------------------FAD_binding_6-1krhB01 B:110-206                                                                  --------NAD_binding_1-1krhB05 B:215-318                                                                         -------------------- Pfam domains (1)
           Pfam domains (2) -------Fer2-1krhB04 B:9-88                                                             ---------------------FAD_binding_6-1krhB02 B:110-206                                                                  --------NAD_binding_1-1krhB06 B:215-318                                                                         -------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee.....eeeeee....hhhhhhhhhh...............eeeeee..ee.hhhhh.....hhhhhhhheee....ee...eeeee....hhhhh...eeeeeeeeeee....eeeeeeee.............eeeee......eeeee........eeeeeee....hhhhhhhhh......eeeeeeee...........eeeeeee.hhhhhhhhhhhhhhhh....eeeeeeeee.hhh.hhhhhhhhhhhh..eeeeeeeee......ee.hhhhh.hhhhhhhhh.eeeeeeehhhhhhhhhhhhhhh....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: B:4-99 UniProt: 14-109                                                        ------FAD_FR  PDB: B:106-207 UniProt: 116-217                                                               ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------2FE2S_FER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1krh B   2 SNHQVALQFEDGVTRFICIAQGETLSDAAYRQQINIPMDCREGECGTCRAFCESGNYDMPEDNYIEDALTPEEAQQGYVLACQCRPTSDAVFQIQASSEVCKTKIHHFEGTLARVENLSDSTITFDIQLDDGQPDIHFLAGQYVNVTLPGTTETRSYSFSSQPGNRLTGFVVRNVPQGKMSEYLSVQAKAGDKMSFTGPFGSFYLRDVKRPVLMLAGGTGIAPFLSMLQVLEQKGSEHPVRLVFGVTQDCDLVALEQLDALQQKLPWFEYRTVVAHAESQHERKGYVTGHIEYDWLNGGEVDVYLCGPVPMVEAVRSWLDTQGIQPANFLFEKFSAN 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_Lum_binding (30)

Family: FAD_binding_6 (24)

Acinetobacter sp. (strain ADP1) (1)

1a	FAD_binding_6-1krhB01	B:110-206
1b	FAD_binding_6-1krhB02	B:110-206

Clan: Fer2 (69)

Family: Fer2 (60)

Acinetobacter sp. (strain ADP1) (1)

2a	Fer2-1krhB03	B:9-88
2b	Fer2-1krhB04	B:9-88

Clan: NAD_Ferredoxin (30)

Family: NAD_binding_1 (30)

Acinetobacter sp. (strain ADP1) (1)

3a	NAD_binding_1-1krhB05	B:215-318
3b	NAD_binding_1-1krhB06	B:215-318

Asymmetric Unit(hide GO term definitions)

Chain A,B (BENC_ACIAD | P07771)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0008860	ferredoxin-NAD+ reductase activity	Catalysis of the reaction: reduced ferredoxin + NAD+ = oxidized ferredoxin + NADH + H+.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042203	toluene catabolic process	The chemical reactions and pathways resulting in the breakdown of toluene, a volatile monoaromatic hydrocarbon found in crude petroleum and petroleum products.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:199 - Pro A:200	[ RasMol ]
		Gly B:199 - Pro B:200	[ RasMol ]

Biological Units
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	1krh
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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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