3T2Z - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF SULFIDE:QUINONE OXIDOREDUCTASE FROM ACIDITHIOBACILLUS FERROOXIDANS

Authors :   M. M. Cherney, Y. Zhang, M. Solomonson, J. H. Weiner, M. N. James

Date :   23 Jul 11 (Deposition) - 17 Aug 11 (Release) - 17 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Oxidoreductase, Sulfide:Quinone Oxidoreductase, Integral Monotopic Membrane Protein, Acidithiobacillus Ferrooxidans (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Cherney, Y. Zhang, M. Solomonson, J. H. Weiner, M. N. James
Crystal Structure Of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans: Insights Into Sulfidotrophi Respiration And Detoxification.
J. Mol. Biol. V. 398 292 2010
PubMed-ID: 20303979 | Reference-DOI: 10.1016/J.JMB.2010.03.018

Molecule 1 - SULFIDE-QUINONE REDUCTASE, PUTATIVE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	469008
	Gene	:	AFE_1792
	Organism Scientific	:	ACIDITHIOBACILLUS FERROOXIDANS
	Organism Taxid	:	243159
	Strain	:	ATCC 23270 / DSM 14882 / NCIB 8455

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 27)

No.	Name	Count	Type	Full Name
1	BU2	2	Ligand/Ion	1,3-BUTANEDIOL
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	H2S	10	Ligand/Ion	HYDROSULFURIC ACID
4	S3H	2	Ligand/Ion	TRISULFANE
5	SO4	11	Ligand/Ion	SULFATE ION

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:7 , GLY A:8 , ALA A:9 , GLY A:10 , THR A:11 , GLY A:12 , SER A:34 , ALA A:35 , VAL A:42 , PRO A:43 , SER A:77 , ALA A:78 , ALA A:104 , THR A:105 , GLY A:106 , PRO A:107 , CYS A:160 , PRO A:163 , GLY A:301 , ILE A:302 , THR A:321 , GLY A:322 , ILE A:325 , VAL A:355 , PHE A:357 , LYS A:391 , S3H A:442 , H2S A:443 , HOH A:465 , BU2 A:502 , HOH A:515 , HOH A:526 , HOH A:542 , HOH A:555 , HOH A:614 , HOH A:618 , HOH A:685 , HOH A:702 , HOH A:734 , HOH A:758	BINDING SITE FOR RESIDUE FAD A 500
02	AC2	SOFTWARE	PRO A:43 , VAL A:355 , PHE A:357 , LYS A:391 , PHE A:394 , MET A:418 , FAD A:500 , HOH A:531 , HOH A:548	BINDING SITE FOR RESIDUE BU2 A 502
03	AC3	SOFTWARE	TYR A:397 , ARG A:400 , LYS A:401 , LYS A:413 , LYS A:417	BINDING SITE FOR RESIDUE SO4 A 435
04	AC4	SOFTWARE	HIS A:334 , ARG A:343 , LYS A:344 , GLY A:345 , GLU A:346	BINDING SITE FOR RESIDUE SO4 A 436
05	AC5	SOFTWARE	LYS A:401 , VAL A:406 , SER A:407 , PRO A:409 , PHE A:410 , LYS A:413	BINDING SITE FOR RESIDUE SO4 A 437
06	AC6	SOFTWARE	TYR A:195 , HIS A:198 , GLN A:202 , GLU A:310 , HOH A:752	BINDING SITE FOR RESIDUE SO4 A 438
07	AC7	SOFTWARE	ARG A:63 , ILE A:74 , ALA A:75 , GLN A:76 , HIS B:72	BINDING SITE FOR RESIDUE SO4 A 439
08	AC8	SOFTWARE	LEU A:109 , SER A:126 , CYS A:128 , THR A:129 , HIS A:132	BINDING SITE FOR RESIDUE H2S A 440
09	AC9	SOFTWARE	CYS A:160 , CYS A:356 , H2S A:441 , H2S A:445 , FAD A:500	BINDING SITE FOR RESIDUE S3H A 442
10	BC1	SOFTWARE	PRO A:163 , GLU A:166 , CYS A:356 , PHE A:357 , S3H A:442 , HOH A:532	BINDING SITE FOR RESIDUE H2S A 441
11	BC2	SOFTWARE	CYS A:356 , H2S A:444 , H2S A:445 , FAD A:500	BINDING SITE FOR RESIDUE H2S A 443
12	BC3	SOFTWARE	CYS A:160 , PRO A:319 , H2S A:443	BINDING SITE FOR RESIDUE H2S A 444
13	BC4	SOFTWARE	GLY A:162 , CYS A:356 , S3H A:442 , H2S A:443 , HOH A:620	BINDING SITE FOR RESIDUE H2S A 445
14	BC5	SOFTWARE	PHE B:41 , PRO B:43 , VAL B:355 , CYS B:356 , PHE B:357 , LYS B:391 , PHE B:394 , MET B:418 , FAD B:500 , HOH B:617	BINDING SITE FOR RESIDUE BU2 B 501
15	BC6	SOFTWARE	LEU B:7 , GLY B:8 , ALA B:9 , GLY B:10 , THR B:11 , GLY B:12 , SER B:34 , ALA B:35 , VAL B:42 , PRO B:43 , SER B:77 , ALA B:78 , ALA B:104 , THR B:105 , GLY B:106 , PRO B:107 , CYS B:128 , CYS B:160 , PRO B:163 , GLY B:301 , ILE B:302 , THR B:321 , GLY B:322 , ILE B:325 , VAL B:355 , PHE B:357 , LYS B:391 , S3H B:442 , H2S B:443 , HOH B:450 , HOH B:474 , HOH B:489 , HOH B:494 , BU2 B:501 , HOH B:608 , HOH B:656 , HOH B:661 , HOH B:726 , HOH B:759	BINDING SITE FOR RESIDUE FAD B 500
16	BC7	SOFTWARE	TYR B:397 , ARG B:400 , LYS B:401 , LYS B:413 , LYS B:417 , ARG B:423	BINDING SITE FOR RESIDUE SO4 B 435
17	BC8	SOFTWARE	HIS A:72 , HOH A:716 , ASP B:37 , ARG B:63 , ALA B:75	BINDING SITE FOR RESIDUE SO4 B 436
18	BC9	SOFTWARE	HIS B:334 , ARG B:343 , LYS B:344 , GLY B:345 , GLU B:346 , GLN B:347	BINDING SITE FOR RESIDUE SO4 B 437
19	CC1	SOFTWARE	TYR B:195 , HIS B:198 , GLN B:202 , GLU B:310 , HOH B:540	BINDING SITE FOR RESIDUE SO4 B 438
20	CC2	SOFTWARE	LYS B:401 , VAL B:406 , SER B:407 , PHE B:410 , LYS B:413	BINDING SITE FOR RESIDUE SO4 B 439
21	CC3	SOFTWARE	LYS B:176 , GLY B:179 , MET B:180 , ARG B:181 , ASP B:182	BINDING SITE FOR RESIDUE SO4 B 440
22	CC4	SOFTWARE	LEU B:109 , SER B:126 , CYS B:128 , THR B:129 , HIS B:132	BINDING SITE FOR RESIDUE H2S B 441
23	CC5	SOFTWARE	CYS B:160 , CYS B:356 , H2S B:445 , H2S B:447 , FAD B:500	BINDING SITE FOR RESIDUE S3H B 442
24	CC6	SOFTWARE	THR B:321 , CYS B:356 , H2S B:444 , H2S B:445 , FAD B:500	BINDING SITE FOR RESIDUE H2S B 443
25	CC7	SOFTWARE	CYS B:160 , H2S B:443 , FAD B:500	BINDING SITE FOR RESIDUE H2S B 444
26	CC8	SOFTWARE	GLY B:162 , CYS B:356 , S3H B:442 , H2S B:443 , HOH B:619	BINDING SITE FOR RESIDUE H2S B 445
27	CC9	SOFTWARE	PRO B:163 , GLU B:166 , CYS B:356 , PHE B:357 , S3H B:442	BINDING SITE FOR RESIDUE H2S B 447

(no "SS Bond" information available for 3T2Z)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:370	-	Pro A:371
2	Lys A:374	-	Pro A:375
3	Gly A:420	-	Ile A:421
4	Leu B:370	-	Pro B:371
5	Lys B:374	-	Pro B:375
6	Gly B:420	-	Ile B:421

(no "SAP(SNP)/Variant" information available for 3T2Z)

(no "PROSITE Motif" information available for 3T2Z)

(no "Exon" information available for 3T2Z)

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:427
 aligned with SQRD_ACIF2 | B7JBP8 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       
           SQRD_ACIF2     1 MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKMMGITRLKEE 427
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh....eeeee...eee...hhhhhh....hhhhheeehhhhhhh...eeee..eeeee....eeee....eee..eeee...eee.hhhh.........ee...hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh.hhhhh..eeeee..............hhhhhhhhhhhhh..eee..eeeeeee..eeeeeee.....eeeeeeee..eeeee..eeehhhhhh........................eee.hhhh................hhhhhhhhhhhhhhhhhhhhh............eeeeee....eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t2z A   1 SAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKMMGITRLKEE 427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with SQRD_ACIF2 | B7JBP8 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       
           SQRD_ACIF2     1 MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKMMGITRLKEE 427
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhh...eeeeee...eee...hhhhhhh...hhhhheeehhhhhhh...eeee..eeeee....eeee....eee..eeee...eee.hhhh.........ee...hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh.hhhhh..eeeee..............hhhhhhhhhhhhh..eee..eeeeeee..eeeeeee.....eeeeeeee..eeeee..eeehhhhhh........................eee.hhhh................hhhhhhhhhhhhhhhhhhhhh............eeeeee....eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t2z B   1 SAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKMMGITRLKEE 427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420

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 "SCOP Domain" information available for 3T2Z)

(no "CATH Domain" information available for 3T2Z)

(no "Pfam Domain" information available for 3T2Z)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SQRD_ACIF2 | B7JBP8)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
	GO:0048038	quinone binding	Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
biological process
	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.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:420 - Ile A:421	[ RasMol ]
		Gly B:420 - Ile B:421	[ RasMol ]
		Leu A:370 - Pro A:371	[ RasMol ]
		Leu B:370 - Pro B:371	[ RasMol ]
		Lys A:374 - Pro A:375	[ RasMol ]
		Lys B:374 - Pro B:375	[ RasMol ]

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	3t2z
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	SQRD_ACIF2 \| B7JBP8	:	3kpk 3sx6 3sxi 3sy4 3syi 3sz0 3szc 3szf 3szw 3t0k 3t14 3t2k 3t2y 3t31

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 27)

Sites (27, 27)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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