2IV2 - JenaLib

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Title :   REINTERPRETATION OF REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI

Authors :   H. C. A. Raaijmakers, M. J. Romao

Date :   08 Jun 06 (Deposition) - 12 Jun 06 (Release) - 19 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.27

Chains :   Asym. Unit : X
Biol. Unit 1: X  (1x)

Keywords :   Oxidoreductase, 4Fe-4S, Naerobic, Complete Proteome, Dehydrogenase, Direct Protein Sequencing, Fe4S4, Formate, Iron, Iron Sulfur Cluster, Iron-Sulfur, Metal-Binding, Mgd, Molybdenum, Molybdopterin, Molybdopterin Guanine Dinucleotide, Mpt, Nad, Secys, Selenium, Selenocysteine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. C. A. Raaijmakers, M. J. Romao
Formate-Reduced E. Coli Formate Dehydrogenase H: The Reinterpretation Of The Crystal Structure Suggests A New Reaction Mechanism.
J. Biol. Inorg. Chem. V. 11 849 2006
PubMed-ID: 16830149 | Reference-DOI: 10.1007/S00775-006-0129-2
(for further references see the PDB file header)

Molecule 1 - FORMATE DEHYDROGENASE H
	Chains	:	X
	EC Number	:	1.2.1.2
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	REDUCED FORM (MO(IV), FE4S4(RED)) OF FDH-H
	Other Details - Source	:	FDH-H WAS EXPRESSED ANAEROBICALLY
	Strain	:	FM911
	Synonym	:	FORMATE-HYDROGEN-LYASE-LINKED, SELENOCYSTEINE- CONTAINING POLYPEPTIDE, FORMATE DEHYDROGENASE-H ALPHA SUBUNIT, FDH-H
	Synthetic	:	YES

		1
Asymmetric Unit	:	X
Biological Unit 1 (1x)	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 6)

No.	Name	Count	Type	Full Name
1	2MD	1	Ligand/Ion	GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
2	MGD	1	Ligand/Ion	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
3	MO	1	Ligand/Ion	MOLYBDENUM ATOM
4	SEC	1	Mod. Amino Acid
5	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER
6	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	2MD	1	Ligand/Ion	GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
2	MGD	1	Ligand/Ion	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
3	MO	-1	Ligand/Ion	MOLYBDENUM ATOM
4	SEC	-1	Mod. Amino Acid
5	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER
6	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS X:8 , TYR X:10 , CYS X:11 , SER X:13 , CYS X:15 , LEU X:41 , CYS X:42 , LYS X:44 , GLY X:45 , PRO X:182 , ILE X:183	BINDING SITE FOR RESIDUE SF4 X 800
2	AC2	SOFTWARE	ARG X:110 , GLY X:111 , THR X:112 , CYS X:136 , GLN X:335 , GLY X:402 , GLU X:403 , ASP X:404 , THR X:408 , ALA X:410 , GLN X:428 , ASP X:429 , ILE X:430 , THR X:433 , SER X:445 , THR X:446 , HIS X:451 , ASP X:478 , CYS X:588 , SER X:590 , TYR X:678 , MGD X:802 , MO X:803 , UNX X:804 , HOH X:2155 , HOH X:2266 , HOH X:2267	BINDING SITE FOR RESIDUE 2MD X 801
3	AC3	SOFTWARE	LYS X:44 , PHE X:173 , GLY X:174 , TYR X:175 , ASN X:176 , ASP X:179 , SER X:180 , CYS X:201 , ASP X:202 , PRO X:203 , ARG X:204 , ILE X:206 , GLY X:221 , ASN X:223 , GLY X:296 , MET X:297 , PHE X:302 , GLY X:334 , THR X:579 , VAL X:580 , ARG X:581 , GLU X:582 , VAL X:583 , HIS X:585 , TYR X:586 , SER X:587 , TYR X:651 , LYS X:679 , 2MD X:801 , MO X:803 , UNX X:804 , HOH X:2082 , HOH X:2084 , HOH X:2125 , HOH X:2259	BINDING SITE FOR RESIDUE MGD X 802
4	AC4	SOFTWARE	2MD X:801 , MGD X:802 , UNX X:804	BINDING SITE FOR RESIDUE MO X 803
5	AC5	SOFTWARE	ALA X:137 , GLY X:334 , 2MD X:801 , MGD X:802 , MO X:803	BINDING SITE FOR RESIDUE UNX X 804

(no "SS Bond" information available for 2IV2)

Asymmetric Unit

No.	Residues
1	Trp X:528	-	Pro X:529
2	Glu X:604	-	Pro X:605

(no "SAP(SNP)/Variant" information available for 2IV2)

Asymmetric Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_MOW_BIS_MGD	PS51669	Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.	FDHF_ECOLI	1-56	1	X:1-56
2	MOLYBDOPTERIN_PROK_1	PS00551	Prokaryotic molybdopterin oxidoreductases signature 1.	FDHF_ECOLI	6-23	1	X:6-23
3	MOLYBDOPTERIN_PROK_2	PS00490	Prokaryotic molybdopterin oxidoreductases signature 2.	FDHF_ECOLI	433-450	1	X:433-450
4	MOLYBDOPTERIN_PROK_3	PS00932	Prokaryotic molybdopterin oxidoreductases signature 3.	FDHF_ECOLI	615-642	1	X:615-642

Biological Unit 1 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_MOW_BIS_MGD	PS51669	Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.	FDHF_ECOLI	1-56	1	X:1-56
2	MOLYBDOPTERIN_PROK_1	PS00551	Prokaryotic molybdopterin oxidoreductases signature 1.	FDHF_ECOLI	6-23	1	X:6-23
3	MOLYBDOPTERIN_PROK_2	PS00490	Prokaryotic molybdopterin oxidoreductases signature 2.	FDHF_ECOLI	433-450	1	X:433-450
4	MOLYBDOPTERIN_PROK_3	PS00932	Prokaryotic molybdopterin oxidoreductases signature 3.	FDHF_ECOLI	615-642	1	X:615-642

(no "Exon" information available for 2IV2)

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 X from PDB  Type:PROTEIN  Length:697
 aligned with FDHF_ECOLI | P07658 from UniProtKB/Swiss-Prot  Length:715

    Alignment length:715
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710     
           FDHF_ECOLI     1 MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVUHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA 715
               SCOP domains d2iv2x2 X:1-564 Formate dehydrogenase H                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             d2iv2x1 X:565-715 Formate dehydrogenase H                                                                                                               SCOP domains
               CATH domains 2iv2X01 X:1-55 ADC-like domains                        -----2iv2X02 X:61-137,X:336-526  [code=3.40.50.740, no name defined]              2iv2X03 X:138-332 Dimethylsulfoxide Reductase, domain 2                                                                                                                                            ---2iv2X02 X:61-137,X:336-526  [code=3.40.50.740, no name defined]                                                                                                                                ---------------------------------------------2iv2X04 X:572-688  [code=2.40.40.20, no name defined]                                                                --------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeeeee..eeeeeee..........hhhhhhhhhhhhh...........ee........ee.hhhhhhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh.....ee............hhhhhhh......hhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhh..eee.....hhhhhhhhhhhhhhhh...hhhhhhhheehhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.hhhhh.hhhhhhhhhhhhhhhh.........eeee....hhhhhhhh.....eehhhee..hhhhhhhhhhhh...........hhhhhhhhhhh....eeeee..hhhhhh.hhhhhhhhhhhh.eeeeee...hhhhhh..eeee........eeee....eeeee...........hhhhhhhhhhhhh.......hhhhhhhhhhhhh......hhhhhh....ee...........................ee..................eeeee...........hhhhhhhhhh......eeeeehhhhhhhh.....eeeee....eeeeeeeee......eeee.....------------------.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_MOW_BIS_MGD  PDB: X:1-56 UniProt: 1-56            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK--------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK_3        ------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----MOLYBDOPTERIN_PROK-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iv2 X   1 MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVxHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWW------------------PEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA 715
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650      |  -         -     | 680       690       700       710     
                                                                                                                                                                     140-SEC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              657                676

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 2IV2)

Asymmetric Unit(hide GO term definitions)

Chain X (FDHF_ECOLI | P07658)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the 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:0008863	formate dehydrogenase (NAD+) activity	Catalysis of the reaction: formate + NAD(+) = CO(2) + NADH.
	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:0030151	molybdenum ion binding	Interacting selectively and non-covalently with molybdenum (Mo) ions.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0015942	formate metabolic process	The chemical reactions and pathways involving formate, also known as methanoate, the anion HCOO- derived from methanoic (formic) acid.
	GO:0015944	formate oxidation	The chemical reactions and pathways by which formate is converted to CO2.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
		Glu X:604 - Pro X:605	[ RasMol ]
		Trp X:528 - Pro X:529	[ RasMol ]

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	2iv2
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	1.2.1.2
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	FDHF_ECOLI \| P07658	:	1aa6 1fdi 1fdo

1aa6	REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI
1fdi	OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE
1fdo	OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI

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Ligands, Modified Residues, Ions (6, 6)

Sites (5, 5)

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