3MTW - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-LYSINE, L-ARGININE CARBOXYPEPTIDASE CC2672 FROM CAULOBACTER CRESCENTUS CB15 COMPLEXED WITH N-METHYL PHOSPHONATE DERIVATIVE OF L-ARGININE

Authors :   A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo

Date :   01 May 10 (Deposition) - 28 Jul 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (8x)

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. F. Xiang, Y. Patskovsky, C. Xu, A. A. Fedorov, E. V. Fedorov, A. A. Sisco, J. M. Sauder, S. K. Burley, S. C. Almo, F. M. Raushel
Functional Identification And Structure Determination Of Tw Novel Prolidases From Cog1228 In The Amidohydrolase Superfamily
Biochemistry V. 49 6791 2010
PubMed-ID: 20604542 | Reference-DOI: 10.1021/BI100897U

Molecule 1 - L-ARGININE CARBOXYPEPTIDASE CC2672
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CC_2672
	Organism Common	:	CAULOBACTER VIBRIOIDES
	Organism Scientific	:	CAULOBACTER VIBRIOIDES
	Organism Taxid	:	155892

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (8x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 20)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	M3R	1	Ligand/Ion	METHYL PHOSPHONATED L-ARGININE
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	7	Ligand/Ion	SULFATE ION
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (5, 36)

No.	Name	Count	Type	Full Name
1	GOL	14	Ligand/Ion	GLYCEROL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	M3R	2	Ligand/Ion	METHYL PHOSPHONATED L-ARGININE
4	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	14	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (5, 144)

No.	Name	Count	Type	Full Name
1	GOL	56	Ligand/Ion	GLYCEROL
2	KCX	8	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	M3R	8	Ligand/Ion	METHYL PHOSPHONATED L-ARGININE
4	PEG	16	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	56	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:90 , HIS A:92 , KCX A:211 , ASP A:344 , M3R A:430	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	KCX A:211 , HIS A:252 , HIS A:272 , M3R A:430	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	ZN A:1 , ZN A:2 , HIS A:90 , HIS A:92 , HIS A:171 , KCX A:211 , GLY A:217 , VAL A:218 , PHE A:219 , HIS A:252 , HIS A:254 , HIS A:272 , ASP A:294 , ASN A:297 , ASP A:318 , ILE A:321 , GLN A:325 , ASP A:344 , HOH A:516 , HOH A:548	BINDING SITE FOR RESIDUE M3R A 430
04	AC4	SOFTWARE	ALA A:256 , ARG A:260 , HOH A:622	BINDING SITE FOR RESIDUE SO4 A 431
05	AC5	SOFTWARE	ARG A:384 , HOH A:672 , HOH A:706 , HOH A:787	BINDING SITE FOR RESIDUE SO4 A 4
06	AC6	SOFTWARE	ARG A:330 , TYR A:363 , HOH A:505 , HOH A:542 , HOH A:768	BINDING SITE FOR RESIDUE SO4 A 5
07	AC7	SOFTWARE	ARG A:57 , TYR A:396 , HOH A:513 , HOH A:775	BINDING SITE FOR RESIDUE SO4 A 6
08	AC8	SOFTWARE	LYS A:30 , ALA A:424 , VAL A:425 , HOH A:671 , HOH A:719	BINDING SITE FOR RESIDUE SO4 A 7
09	AC9	SOFTWARE	ARG A:319 , HOH A:695 , HOH A:762	BINDING SITE FOR RESIDUE SO4 A 8
10	BC1	SOFTWARE	ARG A:384 , TYR A:396 , HOH A:487 , HOH A:769	BINDING SITE FOR RESIDUE SO4 A 9
11	BC2	SOFTWARE	ALA A:150 , GLY A:151 , TYR A:152 , HOH A:727	BINDING SITE FOR RESIDUE GOL A 432
12	BC3	SOFTWARE	ARG A:157 , LYS A:421 , GLY A:422 , HOH A:558 , HOH A:657	BINDING SITE FOR RESIDUE GOL A 433
13	BC4	SOFTWARE	ARG A:145 , ASP A:149 , ARG A:157 , ILE A:158 , VAL A:159 , GLN A:208 , ARG A:384 , HOH A:487 , HOH A:544 , HOH A:611	BINDING SITE FOR RESIDUE GOL A 3
14	BC5	SOFTWARE	VAL A:46 , ASP A:47 , LYS A:63 , HOH A:512 , HOH A:870	BINDING SITE FOR RESIDUE GOL A 434
15	BC6	SOFTWARE	PRO A:186 , PHE A:187 , LYS A:197 , ALA A:198 , THR A:201 , HOH A:591 , HOH A:865	BINDING SITE FOR RESIDUE GOL A 435
16	BC7	SOFTWARE	ASP A:94 , HOH A:563 , HOH A:658 , HOH A:772	BINDING SITE FOR RESIDUE GOL A 436
17	BC8	SOFTWARE	ARG A:36 , GLY A:404 , HOH A:564 , HOH A:565 , HOH A:806 , HOH A:858 , HOH A:873	BINDING SITE FOR RESIDUE GOL A 437
18	BC9	SOFTWARE	GLU A:106 , TYR A:107 , GLU A:146 , HOH A:527 , HOH A:538 , HOH A:725 , HOH A:820 , HOH A:836	BINDING SITE FOR RESIDUE PEG A 438
19	CC1	SOFTWARE	ALA A:67 , VAL A:68 , LYS A:386 , ARG A:395	BINDING SITE FOR RESIDUE PEG A 439

Asymmetric Unit

No.	Residues
1	A:172	-	A:213

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

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

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

(no "Exon" information available for 3MTW)

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
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Chain A from PDB  Type:PROTEIN  Length:403
 aligned with Q9A4Z9_CAUCR | Q9A4Z9 from UniProtKB/TrEMBL  Length:429

    Alignment length:403
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426   
         Q9A4Z9_CAUCR    27 AEIKAVSAARLLDVASGKYVDNPLVIVTDGRITSIGKKGDAVPAGATAVDLPGVTLLPGLIDMHVHLDSLAEVGGYNSLEYSDRFWSVVQTANAKKTLEAGFTTVRNVGAADYDDVGLREAIDAGYVPGPRIVTAAISFGATGGHCDSTFFPPSMDQKNPFNSDSPDEARKAVRTLKKYGAQVIKICATGGVFSRGNEPGQQQLTYEEMKAVVDEAHMAGIKVAAHAHGASGIREAVRAGVDTIEHASLVDDEGIKLAVQKGAYFSMDIYNTDYTQAEGKKNGVLEDNLRKDRDIGELQRENFRKALKAGVKMVYGTDAGIYPHGDNAKQFAVMVRYGATPLQAIQSATLTAAEALGRSKDVGQVAVGRYGDMIAVAGDPLADVTTLEKPVFVMKGGAVVKAP 429
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------Amidohydro_1-3mtwA01 A:81-403                                                                                                                                                                                                                                                                                                      -------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeee.eeeeee..eeeeeee.........eeeeeeeeeeee.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhh......eeee....ee...........hhhhh........hhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhh.eee....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.eee...........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............eeee......hhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mtw A  27 AEIKAVSAARLLDVASGKYVDNPLVIVTDGRITSIGKKGDAVPAGATAVDLPGVTLLPGLIDMHVHLDSLAEVGGYNSLEYSDRFWSVVQTANAKKTLEAGFTTVRNVGAADYDDVGLREAIDAGYVPGPRIVTAAISFGATGGHCDSTFFPPSMDQKNPFNSDSPDEARKAVRTLKKYGAQVIkICATGGVFSRGNEPGQQQLTYEEMKAVVDEAHMAGIKVAAHAHGASGIREAVRAGVDTIEHASLVDDEGIKLAVQKGAYFSMDIYNTDYTQAEGKKNGVLEDNLRKDRDIGELQRENFRKALKAGVKMVYGTDAGIYPHGDNAKQFAVMVRYGATPLQAIQSATLTAAEALGRSKDVGQVAVGRYGDMIAVAGDPLADVTTLEKPVFVMKGGAVVKAP 429
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    |  216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426   
                                                                                                                                                                                                                  211-KCX

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 3MTW)

(no "CATH Domain" information available for 3MTW, only for superseded entry 3GNH replaced by 3MTW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Caulobacter crescentus (Caulobacter vibrioides) (1)

Amidohydro_1-3mtwA01

A:81-403

Asymmetric Unit(hide GO term definitions)

Chain A (Q9A4Z9_CAUCR | Q9A4Z9)


GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mtw)

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3gnh	THE SAME PROTEIN COMPLEXED WITH THE SAME INHIBITOR. THE PREVIOUS REFINEMENT WAS CARRIED OUT WITH CNS AND DID NOT INCLUDE THE NUMBER OF IONS AND LIGANDS. THE PREVIOUS STRUCTURE 3GNH SHOULD BE CONSIDERED AS OBSOLETE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 20)

Sites (19, 19)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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